Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS?
External Email - Use Caution (sorry I split this as an additional email) Though I take your point about testing, although I'd be happy to test in FIPS if it helps our org and others! Also yes, if ultimately it still can't or won't be done, I can look into containers for this client From: fsbuild Sent: Tuesday, July 25, 2023 5:18 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Salomon, Ryan Subject: Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS? My understanding is no environment variable setting like OPENSSL_FIPS=0 will allow md5 or other algorithms found in linux open source code to run which are not allowed under FIPS, e.g., see list, docs.oracle.com/cd/E36784_01/html/E54953/fips-notok-1.html Barring any environment override to turn off FIPS, and assuming you can’t boot into a non-FIPS enabled kernel to run Freesurfer, then one alternative could be to run a container or VM that is not FIPS enabled and in turn run Freesurfer in that. That container/VM could be constrained with specific userids, limited mount points, limited network connections, etc. There are examples of users running (even cloud based) container instances where they need to disable FIPS in order to run software/services, http://secure-web.cisco.com/1iEszMH2CmyG-ljUsLuIW-0dq-aSZ_XApH5MpUsmuTaGagjzGkurggoNzTE6uukka3tNFGgtiDK9K93Phi51jOVRn82inVRr1XSZgHzCoXuNtpU6E9RBfAVTKXJZ6wn7ZvjgyHNtG0mLq8--ZHvPDbdWS9fAs2PSNmQLH2u-5zWMENq5mca9xTxYis0eIqGBUlbqcnl0cxolpzMLzqpdGtCNLxXpsxLrn7qk4iEmBX8bX0Npn3VI-3wd0tf2yYCleKpFQOExyHt3OM2yWsxD2ySqR_KJJSwLuhTJEvrJ6wRUHRMQlBjh5Qc_sTPp7QWCR6v5ahavwRJbUNGZBbIw1sHHSdaa0qJqG9Te9w-us_Co/http%3A%2F%2Fwww.ibm.com%2Fdocs%2Fen%2Fcloud-private%2F3.2.0%3Ftopic%3Dguide-enabling-disabling-fips-mode We currently don’t have resources to test Freesurfer in a FIPS environment. But I would not expect FS to run under FIPS given the list in the above link.. - R. On Jul 24, 2023, at 12:26, Salomon, Ryan wrote: External Email - Use Caution Hello! I'm trying to support our users who use Freesurfer on our systems, but we are trying to keep to a rollout of FIPS, without the need to employ any hacks or the like, and I don't believe non-FIPS is an option on our systems. We still encounter the crypt() error on Freesurfer versions greater than 7.1.1, and again, non-FIPS is likely not an option. There is an environment variable workaround that has been mentioned elsewhere and it doesn't seem to be working for me for mri_deface at least, and again, I really would like to see a word about a proper solution. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1qA7VWJmiC4DgcHOJX79xFlLiYv-WoUTtClaWc9b-wxj1EPndfmsdFP3iodcOwdS4rizXpuc_OKz1oeok2f-lUzf6Tj0iO0x4Ek_0YCGuFQPL9oC9L7gZbXW-ZKQXo4PE6khk2EmY5CSnmL5ekSF9JQ8YjlCdZO3dYuMlZVLFX4YcPDjaf_BD6YRIZ_zcQvU9ywRHSrOXbbRIUDU5yYk7qLXS8Wg0d1P-zOMuULue_Qv1B4iAOXltJqkpYeuPLOixWpzO83M1PTf2uNKqGZQ-TpjLUEfZsvC8mERHmazbunx-cR3tVJN_UhrQ56LLnEKDfqt2zJS9xiNt3Q8tGJjsVQ77jic9N0UaVikBnQj5whk/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1STKczBS_zWGZo3S3eVZrPcN7hmBW68vMzQjzLMY9IPR0DkR5e1g2kJGft79z3WwqmYG4CMIgtG6GH-G8bV4qpj8JLDL5allSJmvyTutuoVO3txf7ciqTWbTvRzUoZeuk71iw-2vS4TTQUoI-ZSHNk5LvP5FeBcd4ESrUJUxyOssBA6IyyAmB40rG545N4aA9xSpwr6QPRILa6RwymnLphVA7K-fJSXrnLZ2KRbpwrStb1z1jV7Hy8IstXfwkVQHFhdVkr63101CCW30Rs1ttBfVM9xHVj8ReBcbaMW1OCF0TAUB3VC8tEt9oDXstNnVD3OLtt5x93bgCurIXEOuZy2pGdaLO7PXVppDXFt1i19k/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!IBzWLUs!RVwAQiJM4ceN3akerTcz1V-4_IH4Q154mux7LKijr_mRjXl_UtXpP8ox0eIhFuIM0_rq_IKJ1a9bUqQVwg$> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS?
External Email - Use Caution Thanks! I suppose my query was ultimately more tightly focused... I was wondering if the issue is confined to a very small amount of code in Freesurfer, such as for the licensing, that could be refactored to use ciphers that are approved under FIPS From: fsbuild Sent: Tuesday, July 25, 2023 5:18 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Salomon, Ryan Subject: Re: [Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS? My understanding is no environment variable setting like OPENSSL_FIPS=0 will allow md5 or other algorithms found in linux open source code to run which are not allowed under FIPS, e.g., see list, docs.oracle.com/cd/E36784_01/html/E54953/fips-notok-1.html Barring any environment override to turn off FIPS, and assuming you can’t boot into a non-FIPS enabled kernel to run Freesurfer, then one alternative could be to run a container or VM that is not FIPS enabled and in turn run Freesurfer in that. That container/VM could be constrained with specific userids, limited mount points, limited network connections, etc. There are examples of users running (even cloud based) container instances where they need to disable FIPS in order to run software/services, http://secure-web.cisco.com/1vEINZo3oeXaEfF8tJ1rZsHwA5ncU6XCBckTtX-aGrsKreVNacE8h-T7ScUXoODFBSDCaNWDYmctMhbIe3AciGNRNVsnWbzVOjrTHsV4CMfvBeKwTxq4adX1Jc15MU1VzbDVybEB_soE43wo2sMeJBoF0C_YmDTA3PRfrfa0xqUd669Gal2D0AoxzgfbEhBcAXvU4y-lmMn5Uv7DoMW3xeYrvuly29ybdE9hrMkJYB3gcWMI_ynbcd9KDDj4v2KjEMX_PbTSDPJVDQGK3O-9JARcpYPcAIsoDbl4avcbSDDyXjWZwvi8u0sovNZEUgwHY6kUgTzDzYUdGZnLifamGXc5mHcjfDtwJYHyZJFlhPB0/http%3A%2F%2Fwww.ibm.com%2Fdocs%2Fen%2Fcloud-private%2F3.2.0%3Ftopic%3Dguide-enabling-disabling-fips-mode We currently don’t have resources to test Freesurfer in a FIPS environment. But I would not expect FS to run under FIPS given the list in the above link.. - R. On Jul 24, 2023, at 12:26, Salomon, Ryan wrote: External Email - Use Caution Hello! I'm trying to support our users who use Freesurfer on our systems, but we are trying to keep to a rollout of FIPS, without the need to employ any hacks or the like, and I don't believe non-FIPS is an option on our systems. We still encounter the crypt() error on Freesurfer versions greater than 7.1.1, and again, non-FIPS is likely not an option. There is an environment variable workaround that has been mentioned elsewhere and it doesn't seem to be working for me for mri_deface at least, and again, I really would like to see a word about a proper solution. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1f9bwxAOty2aIUfKcWHurrBOrN4wNvBlSgr7nkAfsVoMn3vDI1PQr9XMkcYX4wXQkhRu_Va7ZmfAlX4xltjonkRI23l1S-8MGHEbe1pqu69-NC2RiC79K5jKXJ41s63o_meWKS4s4yDAjsXzb_sNGOefqTXw9tGveFw2lokvFvKe2F_KAMwmVH9KPQ8t9fOtol8mtvBRNW9KMU-Soo3XZpF_lLCa305S98LE9j4YCxprGf3ImdDlwxN-86qg7Wn-7mKc6rWxGk3juX5dFu8zNTyvV9tGm8-d0tcw8HroxhwPa2i4sN7wLm14NQwQPFSBzhjBXjLaldILI5Px9xdwKmzURnMk2Qvvt8Rsgv7aLJ2k/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1NephCeZykZm8nZ89bpJeTlomZpwzNMZcxW-GrConT7cbjkOTAcEDC1W8ASbLoPWeh2fW3mGMqfKdz0OPL6P2U1RxkEedlOceYk35hgcnzBzdP-WumANHSBqYvXABuQ53xIzyu1eEerowHu8OEh_zbJYlDLDYkH-6aoWXhtl3GhK273F1t2caOCFg_qy0hT8LOW_onctZERiutUQy-R7Q5El2yW28kp1uTdx4LbX5Y79hPMAHpO75lX2q_f_a2YWxuF6NR0ROifyRUSRqa0aVUVSf9EESzSGnOFMLZYv6NGQWEECWgTnUlikSQ3EmYhrT8GEY9MwpWVzvumvWU71PnNUxc_S4LS0doiO5IQ4u70A/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!IBzWLUs!RVwAQiJM4ceN3akerTcz1V-4_IH4Q154mux7LKijr_mRjXl_UtXpP8ox0eIhFuIM0_rq_IKJ1a9bUqQVwg$> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Any chance at all for an official proper fix for Freesurfer on FIPS?
External Email - Use Caution Hello! I'm trying to support our users who use Freesurfer on our systems, but we are trying to keep to a rollout of FIPS, without the need to employ any hacks or the like, and I don't believe non-FIPS is an option on our systems. We still encounter the crypt() error on Freesurfer versions greater than 7.1.1, and again, non-FIPS is likely not an option. There is an environment variable workaround that has been mentioned elsewhere and it doesn't seem to be working for me for mri_deface at least, and again, I really would like to see a word about a proper solution. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Passcode Request
External Email - Use Caution Hello, I am trying to extract files in the 7zip download for the VurtualBox VM and it requires a passcode. Could you please send me the passcode required for this step. Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] VirtualBox appliance 7z pass code
External Email - Use Caution Hello, any chance I could get the pass code? I'm really hoping to start my project soon, and I haven't been able to get Freesurfer running from scratch. On Fri, Jun 17, 2022 at 2:05 PM Ryan Johnson wrote: > Good afternoon! > > I would like the pass code to unzip the FreeSurfer 7 VirtualBox VM. > > > Thank you, > > Ryan Johnson > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] VirtualBox appliance 7z pass code
External Email - Use Caution Good afternoon! I would like the pass code to unzip the FreeSurfer 7 VirtualBox VM. Thank you, Ryan Johnson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Color LUT after coregister and reslice aparc/aseg.nii
External Email - Use Caution Hello, I'm using fmriprep's aparcaseg_dseg.nii (still FreeSurfer code, right?) to create ROI masks. I wish to coregister and reslice this segmentation file to match the native space for another image (PET), then extract SUVR values for each ROI. However, after coregistration, the lookup values are no longer faithful to their original values. Would there be a way to view or create a new color LUT that reflects that aparcaseg_dseg.nii map in a different space? Thank you, Ryan -- Ryan Wales (he/him), M.A. Ph.D. Candidate Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] smoothing volume data extracted using aparcstats2table
External Email - Use Caution Dear Freesurfer Experts, I am wondering whether the extracted ROI volume data acquired when using the command aparcstats2table needs to be smoothed? I performed surface smoothing using surf2surf for cortical thickness data, but cannot find a way to smooth the volume data listed in aparcstats2table. Is it recommended that I do not perform smoothing? Thank You, Ryan --- Ryan Patrick Bell, Ph.D. Research Analyst, Department of Psychiatry & Behavioral Sciences 905 W. Main St., Suite 24-E Durham, NC 27701 Phone: (919) 681-3495 Email: ryan.b...@duke.edu<mailto:ryan.b...@duke.edu> Website: http://secure-web.cisco.com/1fzJIQLKPmbhrC2x32S5RRIKOnZE7eB318ehdee9qx2NWtarudJFzsrRfGmiqE38f-8rgmwMCQM95jyFZc5NwxcHQjgpXkOexlnYniiTx4ZAVnnhGWIxU2dCKgT1veVi-CoDpm6MVlN2kYuk0D1NhHhyWhG9FDHsjneAtiVRwXvChjCL-aIj41lfCweqI5PvtXo38Y8J8eGmP3nyEsqN6gfjorgZAzVBxkHQHi6bu69EzhbqdnaAK3Fa_0YQQB1nZn4RTTlQTJlTZxExq7YqEtg/http%3A%2F%2Fsites.duke.edu%2Fharp%2F Twitter: twitter.com/HARPatDuke<https://secure-web.cisco.com/1K3qzDbdESi5BxKdIeeFsl0dti1McxRsbgZL6xE6fNf4Bc1Hhc-56u7LgWOmycW3nChbkibU5yMtXl821ohv0XJUC8zoupFj3QfAg1pWDZ67toyio-AWhQM1oZNXaGqlFUzhnPzK2lRLtqZjDeqPfnF7qt1vr54lJlOpIhI38hPSR8U87Fi23jZMIV8bLyeLoA6hjJR8NkLw-p4aowDjK4FoIdlakQqixMWW4tGz96c78qSl5-xIi6RdKXwqX8EfeoqduxrPx4RQb7Ila5xHQKA/https%3A%2F%2Ftwitter.com%2FHARPatDuke> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer on new Mac (apple silicon-chip)
Hi Vânia, Currently, I am running 7.1.1 (the most recent release) on Big Sur without issue. I’m not sure we can speak to the stability when running it on the new Arm chips given they were just released though if you had issues a virtual machine can serve as an alternative. Cheers, Ryan Cali, B.Sc. Research Technician II Center for Neurotechnology and Neurorecovery Laboratory for NeuroImaging of Coma and Consciousness (NICC) Massachusetts General Hospital / Neurology rc...@mgh.harvard.edu<mailto:rc...@mgh.harvard.edu> 978-860-6496 From: freesurfer-boun...@nmr.mgh.harvard.edu Date: Friday, December 4, 2020 at 3:41 AM To: Freesurfer support list Subject: [Freesurfer] Freesurfer on new Mac (apple silicon-chip) External Email - Use Caution Hi, I am about to buy a new laptop and I am wondering if freesurfer will be running on the new mac? I mean, Mac OS big sur (with apple silicon chip, where they no longer use an intel processor). Many thanks for your advice. Best, Vânia de Aguiar, PhD Assistant Professor in Neurolinguistics University of Groningen Faculty of Arts Oude Kijk in 't Jatstraat 26 Room 1315.0408 9712 EK, Groningen The Netherlands ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extracting PET Binding Values from Inflated Surface
External Email - Use Caution Hi Doug, I have a question surrounding our attempts to extract PET binding values (BPND/DVR) which have been first transformed into FS subject space, mapped to the cortical surface using mri_vol2surf (signal averaged over the middle 80% of the cortical ribbon), and then displayed on the inflated hemisphere surfaces. We would like to extract the average binding values from the cortical surface ROIs using the Desikan-Killiany atlas, but are unsure how to go about this. Is there a simple way to use aparcstats2table or a similar command to extract average values from surface ROIs as defined by the ?h.aparc.annot file? Thanks! Ryan O'Dell MD/PhD PGY4 Psychiatry Resident, Yale University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}
Thanks Doug! When you say sample onto the mni152 surface, you mean to use mri_vol2surf, correct? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On May 27, 2020, at 11:10 AM, Douglas N. Greve wrote: > > I would probably run recon-all on the mni152, and then sample the MD map onto > the mni152 surface, then use mris_apply_reg to map it to an individual. > Also, Thomas Yeo has some possibly-better tools to do this. > > On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote: >> Hello FreeSurfer users, >> >> I have a mean diffusivity map that exists in MNI152 space that I want to >> register to a subject’s anatomical space. In the end, I want to display the >> diffusivity on the subject’s surface. I want to ask if this is the correct >> way to do this: >> >> 1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg >> $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create >> registration matrix >> >> 2) mri_vol2vol --mov ./MD.mni152.nii --targ >> $SUBJECTS_DIR/sub-01/mri/brain.mgz --reg >> $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register >> mean diffusivity map to subject space >> >> Thanks in advance, >> >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >> >> >> External Email - Use Caution >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwMDaQ=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=WyIKpFy6Zz_AHJWPenU2h0fVAEZy490shgYvKZ5w1Hs=h0Z_7kcZZRaUYymM_fxyKXtYqN-9wYiD0wU16GwAqjY=> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=WyIKpFy6Zz_AHJWPenU2h0fVAEZy490shgYvKZ5w1Hs=h0Z_7kcZZRaUYymM_fxyKXtYqN-9wYiD0wU16GwAqjY= smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Registering Mean Diffusivity to Anatomical Space
Hello FreeSurfer users, I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this: 1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create registration matrix 2) mri_vol2vol --mov ./MD.mni152.nii --targ $SUBJECTS_DIR/sub-01/mri/brain.mgz --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register mean diffusivity map to subject space Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine
Hi Doug, Here was my original question (we haven't communicated outside of this thread): I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected. This is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Then you asked, "What is the value for cerebellum in those three scenarious (gtm, no pvc, and mgx)?" So I added the uptake values for the cerebellum to the original table, which I've pasted below. Let me know if there's anything else you need. Thanks! Ryan vol | psf | roi | gtmstats_uptake | region_mean ---+---+-+---+--- input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 | 1.226 input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 | 1.0834 input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex | 0.981 | 0.994237 input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 | 1.03552 mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 | 1.00685 mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 | 0.887616 input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 | 1.19702 input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine| 0.47 | 1.05779 input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex | 0.984 | 0.970736 input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 | 1.01104 mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 | 0.915328 mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine| 0.47 | 0.809017 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, April 1, 2020 10:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine Can you include previous emails so that I have some context as to what you are asking? On 4/1/2020 9:18 AM, Eckbo, Ryan wrote: Here's a table with the cerebellum uptake values included -- let me know if you need more information. vol | psf | roi | gtmstats_uptake | region_mean ---+---+-+---+--- input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 | 1.226 input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 | 1.0834 input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex | 0.981 | 0.994237 input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 | 1.03552 mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 | 1.00685 mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 | 0.887616 input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 | 1.19702 input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine| 0.47 | 1.05779 input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex | 0.984 | 0.970736 input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 | 1.01104 mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 | 0.915328 mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine| 0.47 | 0.809017 Thanks! Ryan From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> Sent: Wednesday, March 11, 2020 10:01 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine What is the value for cerebellum in those three scenarious (gtm, no pvc, and mgx)? On 3/10/2020 12:37 PM, Eckbo, Ryan wrote: Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: | vol | psf | roi
Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine
Here's a table with the cerebellum uptake values included -- let me know if you need more information. vol | psf | roi | gtmstats_uptake | region_mean ---+---+-+---+--- input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 | 1.226 input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 | 1.0834 input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex | 0.981 | 0.994237 input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 | 1.03552 mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 | 1.00685 mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 | 0.887616 input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 | 1.19702 input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine| 0.47 | 1.05779 input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex | 0.984 | 0.970736 input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 | 1.01104 mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 | 0.915328 mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine| 0.47 | 0.809017 Thanks! Ryan From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, March 11, 2020 10:01 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine What is the value for cerebellum in those three scenarious (gtm, no pvc, and mgx)? On 3/10/2020 12:37 PM, Eckbo, Ryan wrote: Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: | vol | psf | roi | gtmstats_uptake | mean_uptake | | - | --- | | --- | --- | | input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.226… | | input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 1.083… | | input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 1.197… | | input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 1.058… | | mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.007… | | mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 0.888… | | mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 0.915… | | mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 0.809… | This is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Thanks for any help, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer vol,psf,roi,gtmstats_uptake,region_mean input.rescaled.nii.gz,0,ctx-rh-pericalcarine,0.807,1.2259972095489502 input.rescaled.nii.gz,0,ctx-lh-pericalcarine,0.758,1.083396077156067 input.rescaled.nii.gz,0,Left-Cerebellum-Cortex,0.981,0.9942372441291809 input.rescaled.nii.gz,0,Right-Cerebellum-Cortex,1.0191,1.0355194807052612 mgx.ctxgm.nii.gz,0,ctx-rh-pericalcarine,0.807,1.006852149963379 mgx.ctxgm.nii.gz,0,ctx-lh-pericalcarine,0.758,0.8876161575317383 input.rescaled.nii.gz,6,ctx-rh-pericalcarine,0.409,1.1970176696777344 input.rescaled.nii.gz,6,ctx-lh-pericalcarine,0.47,1.057787299156189 input.rescaled.nii.gz,6,Left-Cerebellum-Cortex,0.9841,0.9707359671592712 input.rescaled.nii.gz,6,Right-Cerebellum-Cortex,1.016,1.0110423564910889 mgx.ctxgm.nii.gz,6,ctx-rh-pericalcarine,0.409,0.9153279066085815 mgx.ctxgm.nii.gz,6,ctx-lh-pericalcarine,0.47,0.8090171217918396 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine
Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: | vol | psf | roi | gtmstats_uptake | mean_uptake | | - | --- | | --- | --- | | input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.226… | | input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 1.083… | | input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 1.197… | | input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 1.058… | | mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.007… | | mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 0.888… | | mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 0.915… | | mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 0.809… | This is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Thanks for any help, Ryan vol,psf,roi,gtmstats_uptake,mean_uptake input.rescaled.nii.gz,0,ctx-rh-pericalcarine,0.807,1.2259972095489502 input.rescaled.nii.gz,0,ctx-lh-pericalcarine,0.758,1.083396077156067 input.rescaled.nii.gz,6,ctx-rh-pericalcarine,0.409,1.1970176696777344 input.rescaled.nii.gz,6,ctx-lh-pericalcarine,0.47,1.057787299156189 mgx.ctxgm.nii.gz,0,ctx-rh-pericalcarine,0.807,1.006852149963379 mgx.ctxgm.nii.gz,0,ctx-lh-pericalcarine,0.758,0.8876161575317383 mgx.ctxgm.nii.gz,6,ctx-rh-pericalcarine,0.409,0.9153279066085815 mgx.ctxgm.nii.gz,6,ctx-lh-pericalcarine,0.47,0.8090171217918396 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] LGI help
Hello Freesurfer users/developers,
I want to run recon-all localGI on a subject who has been processed with
Freesurfer 5.3. Whenever I run recon-all -localGI, I always get an error on
“make_roi_paths”. There error can be found at the end of this email. I looked
at the 5.3 release notes and found the that one issue with localGI was fixed by
substituting a line of code. The current SearchProjectionOnPial.m that I am
using uses this fix.
LGI: issue when using Matlab 2013. the fix is to edit the file
$FREESURFER_HOME/matlab/SearchProjectionOnPial.m and make these changes:
find this line:
< for t=1:step:size(perim,2)
and change to:
> si=max(size(perim));
> for t=1:step:si
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/working/ABCD/FS/NDAR_INV021N0FLH/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_58433_.m');
exit
=
< M A T L A B (R) >
Copyright 1984-2015 The MathWorks, Inc.
R2015b (8.6.0.267246) 64-bit (glnxa64)
August 20, 2015
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
Academic License
>> loading datas ...
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done ( 0.04 sec)
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done ( 0.02 sec)
preparing outer mesh structure ...
face 5000 / 130188
face 1 / 130188
face 15000 / 130188
face 2 / 130188
face 25000 / 130188
face 3 / 130188
face 35000 / 130188
face 4 / 130188
face 45000 / 130188
face 5 / 130188
face 55000 / 130188
face 6 / 130188
face 65000 / 130188
face 7 / 130188
face 75000 / 130188
face 8 / 130188
face 85000 / 130188
face 9 / 130188
face 95000 / 130188
face 10 / 130188
face 105000 / 130188
face 11 / 130188
face 115000 / 130188
face 12 / 130188
face 125000 / 130188
face 13 / 130188
mesh_outer =
vertices: [65096x3 double]
faces: [130188x3 double]
facesOfVertex: [65096x1 struct]
preparing pial mesh structure ...
...searching for mesh edges...done (134.42 sec).
... creating path file for vertex 1 / 65096
area file for outer ROIs saved at 1
In an assignment A(:) = B, the number of elements in A and B must be the same.
Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));
Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);
Error in reorganize_verticeslist (line 28)
[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);
>>
ERROR: make_roi_paths did not complete successfully!
Linux jamestown.radiology.ucsf.edu 3.10.0-1062.1.2.el7.x86_64 #1 SMP Mon Sep 16
14:19:51 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s NDAR_INV021N0FLH exited with ERRORS at Tue Mar 3 11:09:41 PST 2020
For more details, see the log file
/working/ABCD/FS/NDAR_INV021N0FLH/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thank you for your time,
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging
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[Freesurfer] freesurfer linux-ppc build
External Email - Use Caution Hello, Is there an available freesurfer linux power pc (Power 9) build? I can not find any information about this online. If not , I have been working on making one and would like to know if anyone else has any progress ... Thanks, Ryan Schneider Boston University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}
External Email - Use Caution Thanks, Doug. One more question: I want to see how correlated my covariate ROI is with LGI and compare the correlation maps between the two groups. Is my glmfit command the correct setup? I have tried running glmfit on a different fsgd and contrast matrix with only one of the two groups and have a pcc.mgh for that analysis. When I compare that to the pcc.mgh I get from my original analysis for that same group, the value at each vertex is slightly different. Ryan Michael Nillo UCSF Department is Radiology and Biomedical Imaging Lab for Precision Neuroimaging Staff Research Associate 1 > On Oct 28, 2019, at 11:17, Greve, Douglas N.,Ph.D. > wrote: > > Yes > >> On 10/28/19 1:04 PM, Nillo, Ryan Michael R wrote: >> Am I correct in assuming this results in z-scoring/normalizing the >> covariates? >> >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >>> On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D. >>> mailto:dgr...@mgh.harvard.edu>> wrote: >>> >>> My guess is that your covariates have almost no range to them and so >>> look like constant (similar to columns 1 and 2). You can try >>> demeaning and rescaling the covariates. You can do this by hand and >>> create a new FSGD file or you can add the following lines anywhere in >>> the fsgd: >>> RescaleFlag 1 >>> DemeanFlag 1 >>> >>> >>> On 10/26/19 10:45 PM, Nillo, Ryan Michael R wrote: >>>> Hello, >>>> >>>> I ran mri_glmfit with the following fsgd file: >>>> >>>> GroupDescriptorFile 1 >>>> Title CJD >>>> >>>> Class MM1_MV1 >>>> Class MV2_VV2 >>>> >>>> Variablesfrontal >>>> >>>> Input7693MV2_VV22.930667 >>>> Input11985MV2_VV22.410333 >>>> Input13082MV2_VV22.529333 >>>> Input13425MV2_VV22.593667 >>>> Input13667MM1_MV12.628667 >>>> Input13900MM1_MV12.675333 >>>> Input14094MM1_MV12.549333 >>>> Input15566MV2_VV22.67 >>>> Input15999MM1_MV12.641 >>>> Input16714MV2_VV22.643 >>>> Input16848MV2_VV22.63 >>>> Input16952MV2_VV22.516 >>>> Input7693aMV2_VV23.054 >>>> Input11985aMV2_VV22.42 >>>> Input13082aMV2_VV22.454 >>>> Input13425aMV2_VV22.602 >>>> Input13667aMM1_MV12.604333 >>>> Input13900aMM1_MV12.601333 >>>> Input14094aMM1_MV12.52 >>>> Input15566aMV2_VV22.71 >>>> Input15999aMM1_MV12.584333 >>>> Input16714aMV2_VV22.67 >>>> Input16848aMV2_VV22.53 >>>> Input16952aMV2_VV22.486 >>>> >>>> My two contrast matrices are: >>>> one.mtx = [ 0 0 1 0 ] >>>> two.mtx = [ 0 0 0 1 ] >>>> >>>> When running the mri_glmfit command "*mri_glmfit --glmdir >>>> new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 30 --surf >>>> fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx*”, I >>>> get the following output: >>>> >>>> INFO: gd2mtx_method is dods >>>> Saving design matrix to new.frontal.lgi/Xg.dat >>>> Computing normalized matrix >>>> Normalized matrix condition is 12820.7 >>>> Design matrix -- >>>> 0.0 1.0 0.0 2.93067; >>>> 0.0 1.0 0.0 2.41033; >>>> 0.0 1.0 0.0 2.52933; >>>> 0.0 1.0 0.0 2.59367; >>>> 1.0 0.0 2.62867 0.0; >>>> 1.0 0.0 2.67533 0.0; >>>> 1.0 0.0 2.54933 0.0; >>>> 0.0 1.0 0.0 2.7; >>>> 1.0 0.0 2.64100 0.0; >>>> 0.0 1.0 0.0 2.64300; >>>> 0.0 1.0 0.0 2.63000; >>>> 0.0 1.0 0.0 2.51600; >>>> 0.0 1.0 0.0 3.05400; >>>> 0.0 1.0 0.0 2.42000; >>>> 0.0 1.0 0.0 2.45400; >>>> 0.0 1.0 0.0 2.60200; >>>> 1.0 0.0 2.60433 0.0; >>>> 1.0 0.0 2.60133 0.0; >>>> 1.0 0.0 2.52333 0.0; >>>> 0.0 1.0 0.0 2.71333; >>>> 1.0 0.0 2.58433 0.0; >>>> 0.0 1.0 0.
Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}
Am I correct in assuming this results in z-scoring/normalizing the covariates? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D. > wrote: > > My guess is that your covariates have almost no range to them and so look > like constant (similar to columns 1 and 2). You can try demeaning and > rescaling the covariates. You can do this by hand and create a new FSGD file > or you can add the following lines anywhere in the fsgd: > RescaleFlag 1 > DemeanFlag 1 > > > On 10/26/19 10:45 PM, Nillo, Ryan Michael R wrote: >> Hello, >> >> I ran mri_glmfit with the following fsgd file: >> >> GroupDescriptorFile 1 >> Title CJD >> >> Class MM1_MV1 >> Class MV2_VV2 >> >> Variables frontal >> >> Input 7693 >> MV2_VV2 2.930667 >> Input 11985 >> MV2_VV2 2.410333 >> Input 13082 >> MV2_VV2 2.529333 >> Input 13425 >> MV2_VV2 2.593667 >> Input 13667 >> MM1_MV1 2.628667 >> Input 13900 >> MM1_MV1 2.675333 >> Input 14094 >> MM1_MV1 2.549333 >> Input 15566 >> MV2_VV2 2.67 >> Input 15999 >> MM1_MV1 2.641 >> Input 16714 >> MV2_VV2 2.643 >> Input 16848 >> MV2_VV2 2.63 >> Input 16952 >> MV2_VV2 2.516 >> Input 7693a >> MV2_VV2 3.054 >> Input 11985a >> MV2_VV2 2.42 >> Input 13082a >> MV2_VV2 2.454 >> Input 13425a >> MV2_VV2 2.602 >> Input 13667a >> MM1_MV1 2.604333 >> Input 13900a >> MM1_MV1 2.601333 >> Input 14094a >> MM1_MV1 2.52 >> Input 15566a >> MV2_VV2 2.71 >> Input 15999a >> MM1_MV1 2.584333 >> Input 16714a >> MV2_VV2 2.67 >> Input 16848a >> MV2_VV2 2.53 >> Input 16952a >> MV2_VV2 2.486 >> >> My two contrast matrices are: >> one.mtx = [ 0 0 1 0 ] >> two.mtx = [ 0 0 0 1 ] >> >> When running the mri_glmfit command "mri_glmfit --glmdir new.frontal.lgi >> --fsgd new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y >> lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx”, I get the following output: >> >> INFO: gd2mtx_method is dods >> Saving design matrix to new.frontal.lgi/Xg.dat >> Computing normalized matrix >> Normalized matrix condition is 12820.7 >> Design matrix -- >> 0.0 1.0 0.0 2.93067; >> 0.0 1.0 0.0 2.41033; >> 0.0 1.0 0.0 2.52933; >> 0.0 1.0 0.0 2.59367; >> 1.0 0.0 2.62867 0.0; >> 1.0 0.0 2.67533 0.0; >> 1.0 0.0 2.54933 0.0; >> 0.0 1.0 0.0 2.7; >> 1.0 0.0 2.64100 0.0; >> 0.0 1.0 0.0 2.64300; >> 0.0 1.0 0.0 2.63000; >> 0.0 1.0 0.0 2.51600; >> 0.0 1.0 0.0 3.05400; >> 0.0 1.0 0.0 2.42000; >> 0.0 1.0 0.0 2.45400; >> 0.0 1.0 0.0 2.60200; >> 1.0 0.0 2.60433 0.0; >> 1.0 0.0 2.60133 0.0; >> 1.0 0.0 2.52333 0.0; >> 0.0 1.0 0.0 2.71333; >> 1.0 0.0 2.58433 0.0; >> 0.0 1.0 0.0 2.67333; >> 0.0 1.0 0.0 2.5; >> 0.0 1.0 0.0 2.48600; >> >> ERROR: matrix is ill-conditioned or badly scaled, condno = 12820.7 >> >> Possible problem with experimental design: >> Check for duplicate entries and/or lack of range of >> continuous variables within a class. >> If you seek help with this problem, make sure to send: >> 1. Your command line: >> mri_glmfit --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm >> 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx >> 2. The FSGD file (if using one) >> 3. And the design matrix above >> Attempting to diagnose further >> SumSq: Min=2.828427 (col 1), Max=10.485683 (col 4) >> ... could not determine the cause of the problem >> >> >> Can anyone give me some insight into what might be going wrong? >> >> Thanks so much, >> >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >> >>
[Freesurfer] mri_glmfit ill-conditioned matrix question
Hello, I ran mri_glmfit with the following fsgd file: GroupDescriptorFile 1 Title CJD Class MM1_MV1 Class MV2_VV2 Variables frontal Input 7693MV2_VV2 2.930667 Input 11985 MV2_VV2 2.410333 Input 13082 MV2_VV2 2.529333 Input 13425 MV2_VV2 2.593667 Input 13667 MM1_MV1 2.628667 Input 13900 MM1_MV1 2.675333 Input 14094 MM1_MV1 2.549333 Input 15566 MV2_VV2 2.67 Input 15999 MM1_MV1 2.641 Input 16714 MV2_VV2 2.643 Input 16848 MV2_VV2 2.63 Input 16952 MV2_VV2 2.516 Input 7693a MV2_VV2 3.054 Input 11985a MV2_VV2 2.42 Input 13082a MV2_VV2 2.454 Input 13425a MV2_VV2 2.602 Input 13667a MM1_MV1 2.604333 Input 13900a MM1_MV1 2.601333 Input 14094a MM1_MV1 2.52 Input 15566a MV2_VV2 2.71 Input 15999a MM1_MV1 2.584333 Input 16714a MV2_VV2 2.67 Input 16848a MV2_VV2 2.53 Input 16952a MV2_VV2 2.486 My two contrast matrices are: one.mtx = [ 0 0 1 0 ] two.mtx = [ 0 0 0 1 ] When running the mri_glmfit command "mri_glmfit --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx”, I get the following output: INFO: gd2mtx_method is dods Saving design matrix to new.frontal.lgi/Xg.dat Computing normalized matrix Normalized matrix condition is 12820.7 Design matrix -- 0.0 1.0 0.0 2.93067; 0.0 1.0 0.0 2.41033; 0.0 1.0 0.0 2.52933; 0.0 1.0 0.0 2.59367; 1.0 0.0 2.62867 0.0; 1.0 0.0 2.67533 0.0; 1.0 0.0 2.54933 0.0; 0.0 1.0 0.0 2.7; 1.0 0.0 2.64100 0.0; 0.0 1.0 0.0 2.64300; 0.0 1.0 0.0 2.63000; 0.0 1.0 0.0 2.51600; 0.0 1.0 0.0 3.05400; 0.0 1.0 0.0 2.42000; 0.0 1.0 0.0 2.45400; 0.0 1.0 0.0 2.60200; 1.0 0.0 2.60433 0.0; 1.0 0.0 2.60133 0.0; 1.0 0.0 2.52333 0.0; 0.0 1.0 0.0 2.71333; 1.0 0.0 2.58433 0.0; 0.0 1.0 0.0 2.67333; 0.0 1.0 0.0 2.5; 0.0 1.0 0.0 2.48600; ERROR: matrix is ill-conditioned or badly scaled, condno = 12820.7 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --glmdir new.frontal.lgi --fsgd new.frontal.fsgd.txt --fwhm 30 --surf fsaverage lh --y lh.pial_lgi.fwhm0.mgh --C one.mtx --C two.mtx 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=2.828427 (col 1), Max=10.485683 (col 4) ... could not determine the cause of the problem Can anyone give me some insight into what might be going wrong? Thanks so much, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question on Z-scoring
Hello FreeSurfer users/devs, I have a question on z-scoring. I would like to produce z-scored volume maps for each subject in my study. Is my process correct? 1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume —tval $sub/surf/$h.volume.mgh —sfmt curv (convert .volume file to .mgh file) 2) mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume --mean --fwhm 0 --o $PWD/$h.volume.pop_mean.mgh (obtain mean population volume at each vertex) 3) mris_preproc --hemi $h --fsgd 09172019.fsgd.txt --meas volume —std --fwhm 0 --o $PWD/$h.volume.pop_std.mgh (obtain volume standard deviation volume at each vertex) 4) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval $PWD/$h.volume.pop_mean.mgh —tval $sub/surf/$h.volume.pop_mean.mgh —hemi $h (map population mean to subject space) 5) mri_surf2surf —srcsubject fsaverage —trgsubject $sub —sval $PWD/$h.volume.pop_std.mgh —tval $sub/surf/$h.volume.pop_std.mgh —hemi $h (map population std to subject space) 6) fscalc $sub/surf/$h.volume.mgh sub $sub/surf/$h.volume.pop_mean.mgh div $sub/surf/$h.volume.pop_std.mgh -o $sub/surf/$h.volume_z.mgh 7) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $sub/surf/$h.volume_z.mgh —tval $sub/surf/$h.volume_z —tfmt curv (convert .mgh to curv file) After z-scoring each vertex, I want to do a group analysis between the two groups in my cohort. Instead of using raw volume as my measurement, I would be using z-scored volume. Thanks for the help, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Converting a binary overlay file to label
External Email - Use Caution Hello FreeSurfer users/developers. I manually created a binary overlay file on the pial surface. I am interested in looking at regions outside of this overlay file, so I converted lh.cortex.label to a binary overlay file and took the difference between the two. I want to take this new file and create a label so that I can run mris_anatomical_stats on the new region. How might I do this? Sent from my iPhone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed} {Disarmed}
Pial-outer-smoothed was a surface created from recon-all -localGI. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Jul 1, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D. > wrote: > > how was pial-outer-smoothed create? > > On 7/1/2019 2:33 PM, Nillo, Ryan Michael R wrote: >> Hi Doug, >> >> lh.test.nii was created with: >> >> mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 >> --regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o >> ./lh.test.nii >> >> Where lh.probability.nii is a probability mask created from about 63 >> subjects. >> >> Thanks in advance for the help, >> >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >>> On Jul 1, 2019, at 11:13 AM, Greve, Douglas N.,Ph.D. >>> mailto:dgr...@mgh.harvard.edu>> wrote: >>> >>> Who did you create lh.test.nii? >>> >>> On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote: >>>> Hi Bruce, >>>> >>>> We wanted to map values from a previous analysis to a representation of >>>> the brain with the sulci filled — something that resembles the output >>>> lh.pial-outer-smoothed from the recon-all -localGI. I tried using >>>> mri_surf2surf, but I get the error: >>>> >>>> ERROR: dimension inconsistency in source data >>>>Number of surface vertices = 163842 >>>>Number of value vertices = 73466 >>>> >>>> My command: mri_surf2surf --srcsubject fsaverage_1 --trgsubject fsaverage >>>> --sval ./lh.test.nii --tval lh.pial-outer-smoothed2white.nii --hemi lh >>>> >>>> fsaverage_1 is a copy of fsaverage that I ran recon-all -localGI on to get >>>> the pial-outer-smoothed surface. >>>> Ryan Michael Nillo >>>> Staff Research Associate I >>>> University of California San Francisco >>>> Department of Radiology and Biomedical Imaging >>>> >>>>> On Jul 1, 2019, at 10:27 AM, Bruce Fischl >>>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >>>>> >>>>> Hi Ryan >>>>> >>>>> I'm not sure why you would have a surface with 73K vertices on fsaverage. >>>>> Why not use one of the ico representations (40K or 160K vertices)? In any >>>>> case, mri_surf2surf should do the trick, although you will probably need >>>>> to create a new subject with a set of 73K vertex surfaces >>>>> >>>>> cheers >>>>> Bruce >>>>> On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote: >>>>> >>>>>> Hello Freesurfer users/developers, >>>>>> I have surface with ~73,400 vertices generated from the Freesurfer >>>>>> version 6 >>>>>> fsaverage brain, left hemisphere. I have a surface map that was created >>>>>> by >>>>>> mapping a volume to the fsaverage white surface. Is there a way to map >>>>>> the >>>>>> surface map to the new surface with less vertices? Is there a way to map >>>>>> values from the 73,000 vertices-map to the standard fsaverage pal >>>>>> surface? >>>>>> Thanks in advance, >>>>>> Ryan Michael Nillo >>>>>> Staff Research Associate I >>>>>> University of California San Francisco >>>>>> Department of Radiology and Biomedical Imaging >>>>> ___ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow= >>>>> >>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow=> >>>> >>>> >>>> External Email - Use Caution
Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}
Hi Doug, lh.test.nii was created with: mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 --regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o ./lh.test.nii Where lh.probability.nii is a probability mask created from about 63 subjects. Thanks in advance for the help, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Jul 1, 2019, at 11:13 AM, Greve, Douglas N.,Ph.D. > wrote: > > Who did you create lh.test.nii? > > On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote: >> Hi Bruce, >> >> We wanted to map values from a previous analysis to a representation of the >> brain with the sulci filled — something that resembles the output >> lh.pial-outer-smoothed from the recon-all -localGI. I tried using >> mri_surf2surf, but I get the error: >> >> ERROR: dimension inconsistency in source data >>Number of surface vertices = 163842 >>Number of value vertices = 73466 >> >> My command: mri_surf2surf --srcsubject fsaverage_1 --trgsubject fsaverage >> --sval ./lh.test.nii --tval lh.pial-outer-smoothed2white.nii --hemi lh >> >> fsaverage_1 is a copy of fsaverage that I ran recon-all -localGI on to get >> the pial-outer-smoothed surface. >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >>> On Jul 1, 2019, at 10:27 AM, Bruce Fischl >> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >>> >>> Hi Ryan >>> >>> I'm not sure why you would have a surface with 73K vertices on fsaverage. >>> Why not use one of the ico representations (40K or 160K vertices)? In any >>> case, mri_surf2surf should do the trick, although you will probably need to >>> create a new subject with a set of 73K vertex surfaces >>> >>> cheers >>> Bruce >>> On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote: >>> >>>> Hello Freesurfer users/developers, >>>> I have surface with ~73,400 vertices generated from the Freesurfer version >>>> 6 >>>> fsaverage brain, left hemisphere. I have a surface map that was created by >>>> mapping a volume to the fsaverage white surface. Is there a way to map the >>>> surface map to the new surface with less vertices? Is there a way to map >>>> values from the 73,000 vertices-map to the standard fsaverage pal surface? >>>> Thanks in advance, >>>> Ryan Michael Nillo >>>> Staff Research Associate I >>>> University of California San Francisco >>>> Department of Radiology and Biomedical Imaging >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow= >>> >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow=> >> >> >> External Email - Use Caution >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwMGaQ=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=KZafiDpWfd1AKhGg8N3guW90iGbHCnKbiayUEjeKvhg=EA1H4VuXjUSeBglZfSe-BxQKIubSYpJUk6ZYumGjoo8=> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=KZafiDpWfd1AKhGg8N3guW90iGbHCnKbiayUEjeKvhg=EA1H4VuXjUSeBglZfSe-BxQKIubSYpJUk6ZYumGjoo8= smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Surfaces with different numbers of vertices.
Hi Bruce, We wanted to map values from a previous analysis to a representation of the brain with the sulci filled — something that resembles the output lh.pial-outer-smoothed from the recon-all -localGI. I tried using mri_surf2surf, but I get the error: ERROR: dimension inconsistency in source data Number of surface vertices = 163842 Number of value vertices = 73466 My command: mri_surf2surf --srcsubject fsaverage_1 --trgsubject fsaverage --sval ./lh.test.nii --tval lh.pial-outer-smoothed2white.nii --hemi lh fsaverage_1 is a copy of fsaverage that I ran recon-all -localGI on to get the pial-outer-smoothed surface. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging > On Jul 1, 2019, at 10:27 AM, Bruce Fischl wrote: > > Hi Ryan > > I'm not sure why you would have a surface with 73K vertices on fsaverage. Why > not use one of the ico representations (40K or 160K vertices)? In any case, > mri_surf2surf should do the trick, although you will probably need to create > a new subject with a set of 73K vertex surfaces > > cheers > Bruce > On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote: > >> Hello Freesurfer users/developers, >> I have surface with ~73,400 vertices generated from the Freesurfer version 6 >> fsaverage brain, left hemisphere. I have a surface map that was created by >> mapping a volume to the fsaverage white surface. Is there a way to map the >> surface map to the new surface with less vertices? Is there a way to map >> values from the 73,000 vertices-map to the standard fsaverage pal surface? >> Thanks in advance, >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow= smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Surfaces with different numbers of vertices.
Hello Freesurfer users/developers, I have surface with ~73,400 vertices generated from the Freesurfer version 6 fsaverage brain, left hemisphere. I have a surface map that was created by mapping a volume to the fsaverage white surface. Is there a way to map the surface map to the new surface with less vertices? Is there a way to map values from the 73,000 vertices-map to the standard fsaverage pal surface? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Help for smoothing the pial surface
Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI <https://surfer.nmr.mgh.harvard.edu/fswiki/LGI>) without having to run the entire recon-all process. Additionally, I want to map this surface to the white surface. Is there an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Smoothing the pill surface
Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) without having to run the entire recon-all process. Additionally, I want to map this surface to the white surface. Is there an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Projecting subcortical ROI to the cortical surface
External Email - Use Caution Hi Bruce, We want to study whether or not presence of periventricular heterotopias affect the thickness, volume, or surface area of the nearest cortical ROI. Since the condition we are studying is caused by failure of neurons to migrate to the cortex, we hypothesized that the nearest cortical ROI would be thinner/smaller compared to those without the heterotopia. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On May 15, 2019, at 3:10 PM, Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Ryan I don't think projection of that kind of ROI is well-posed. Different parts of it are probably closest to wildly different parts of cortex. What are you trying to acheive? cheers Bruce On Wed, 15 May 2019, Nillo, Ryan Michael R wrote: External Email - Use Caution Hello FreeSurfer users/developers, I have a subcortical ROI that I want to project to the nearest cortical vertex (see screenshot). So far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to project these voxels to the nearest vertex on the cortex. I am not sure if this is the correct way to do this because using mris_anatomical_stats on the result does not produce any thickness file. Any help would be greatly appreciated. [IMAGE] Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwICAg=iORugZls2LlYyCAZRB3XLg=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U=70PkXR7pfoOtgUn0p3XVxYSvqoKz7NOM0ksGg_OyUmg=4-bL_WUolc7CdEE6RovlOGA5oFWwlecwJNlG57CXOR0= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Color scale error
External Email - Use Caution Toggling the colorbar on and off in the GUI updates the values and appearance. Changing the threshold also seems to work once I press the “apply” button on the configuration window. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On May 1, 2019, at 12:52 PM, Ruopeng Wang wrote: Can you try turning off/on the scale bar or change the threshold a little bit and see if it updates? Ruopeng On May 1, 2019, at 2:48 PM, Nillo, Ryan Michael R mailto:ryanmichael.ni...@ucsf.edu>> wrote: External Email - Use Caution Hello FreeSurfer Developers. I am using FSv6 and I am having problems loading a colorbar. I am trying to run this code: freeview -f /data/sugrue2/ABCD/fsaverage/surf/rh.pial:overlay=/data/sugrue2/ABCD/temp/testing.mgh:overlay_threshold=0,1:overlay_method=linear -viewport 3d -hide-3d-slices -nocursor —colorscale. The resulting color scale makes no sense in that it does not properly display the min and max values specified. As you can see in the screenshot, the color scale runs from 1e-10 to -1e-10. Configuring the colors from the GUI seems to fix the issue, but Ideally I would like to automate the screenshot process. Any help is greatly appreciated. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Obtaining stats for a custom label
External Email - Use Caution Correction to the previous email: I can view the label in the rh.white, not lh.white. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On Apr 24, 2019, at 10:50 AM, Nillo, Ryan Michael R mailto:ryanmichael.ni...@ucsf.edu>> wrote: lh.white surface ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Obtaining stats for a custom label
External Email - Use Caution Hi Doug, I used the command below to convert a volume to a label file. The volume is a binary mask highlighting a subcortical ROI that I am projecting to the closest vertex. I can visualize the label on the fsaverage lh.white surface. mri_vol2label --i /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/rh.custom.nii --id 1 --l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On Apr 24, 2019, at 9:48 AM, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: How did you create the label? Is it a surface-based label? Ie, does it have valid vertex indices as the first item in each label point in the label file? On 4/24/2019 2:44 AM, Nillo, Ryan Michael R wrote: External Email - Use Caution Hello Freesurfer developers, I am using the code below to generate the stats table for the ROI. mris_anatomical_stats -l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label -b subject rh white However, when I run this command, I get this output: limiting computations to label /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label. reading volume /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz... reading input surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... reading input pial surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial... reading input white surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name I am getting no values for any of the metrics listed above. Is this a bug? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Obtaining stats for a custom label
External Email - Use Caution Hello Freesurfer developers, I am using the code below to generate the stats table for the ROI. mris_anatomical_stats -l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label -b subject rh white However, when I run this command, I get this output: limiting computations to label /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label. reading volume /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz... reading input surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... reading input pial surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial... reading input white surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name I am getting no values for any of the metrics listed above. Is this a bug? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Projecting a subcortical label to the surface
External Email - Use Caution Hello FreeSurfer users, I have a subcortical segmentation that I want to project to the nearest cortical vertex. Would I use the mri_vol2surf command to accomplish this, or do I need to convert the segmentation into a label, then project the label to the fsaverage cortical surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_vol2surf error
External Email - Use Caution Hello FS users, I am having a problem with mri_vol2surf. I want to project subcortical voxels onto the cortical surface. I found out that I can do this with the mri_vol2surf command. I am following the example given on the documentation, but I am getting this error: mri_vol2surf: could not read surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc//surf/lh.white. I am trying to project to the surface of the fsaverage. Does this error mean that FS is unable to find the fsaverage surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] pial surface and eTIV
External Email - Use Caution Hello, I'm using freesurfer ver 6.0.0. If there are defects with the pial surface (i.e. the pial surface does not cover all the gray matter that it should), can you also assume that the eTIV has not been estimated incorrectly, or do pial surface inaccuracies not indicate eTIV inaccuracy? I know eTIV is estimated based on the linear transform to the talairach.xfm, but I'm not sure if there's any way to determine eTIV accuracy directly. I'm quality checking my images and am curious if I should remove subjects based on poor pial surfaces or if that does not matter. Important to note, at the moment, I'm only interested in pulling hippocampal volumes and eTIV (to get relative hippocampal volumes). Similarly, would poor pial segmentation affect the reported hippocampal volumes at all? What do you recommend? Thanks, Ryan -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Color scale is off
External Email - Use Caution Hello FreeSurfer users, I am using FreeSurfer version 6 with the latest dev version of freeview on a Linux machine. When I load a surface into freeview with a color scale, I notice the scale does not correlate with the values in the surface. The min and max values are always some small number (e.g. 3.0 x 10^-6). This happens even if I set the threshold in the command line. To fix it, I would need to configure the surface and click “apply”. In the past, the color scale would format itself correctly without me having to go through that configure step. Example command line: freeview -f fsaverage/surf/ph.pial:overlay=lh.thickness.betas:overlay_threshold=0,0.05:overlay_method=linear -colorscale -ss lh.lateral.thickness.beta.tiff Thanks in advance, Ryan Nillo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Should I edit or reject?
External Email - Use Caution Hi, Although there are many ways to correct for pial, WM, and segmentation defects, it seems common in the literature to forego any edits and simply either accept or reject a subject's FreeSurfer output in order to avoid subjectivity and potential over-editing. Another group rejected subjects if their defects spanned 6 or more slices, for example. Are there any guide lines on how much editing is too much editing? Should it just be edited enough so it looks tolerable by eye? Maybe by a few different raters? The defects vary in their severity, so it's difficult to know if a subject should be considered passable or requiring edits based on a minor defect. My current plan is to conduct my analysis once with excluding subjects with poor segmentation and then again, including those subjects' edited outputs. Do you agree with this logic? Thanks for your advice, Ryan -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Setting the origin in native space
External Email - Use Caution Thanks for your help, Bruce. This worked like a charm! How would I register the output segmentation back to the subject's T1.mgz? When I use mri_convert, the ROIs have a weird border around them. thanks again, Ryan From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Wednesday, December 19, 2018 11:43:03 AM To: Freesurfer support list Subject: Re: [Freesurfer] Setting the origin in native space Hi Ryan I think mri_convert -at should do the trick. cheers Bruce On Wed, 19 Dec 2018, Nillo, Ryan Michael R wrote: >External Email - Use Caution > > Hello FreeSurfer users, > > I want to use the suit software to segment the cerebellum, however the > software requires the origin be set at the anterior composure. I know the > Talairach image’s origin is set at the anterior commisure and that there is a > Talairach transformation in mri/transforms. Is there a way to use this > information to set the origin to the anterior commisure in the native space > image? > > Thanks in advance, > Ryan Nillo > Staff Research Associate > UCSF Department of Radiology and Biomedical Imaging > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives.. A searchable archive which of messages PRIOR to March 2004 is at this site A searchable archive which includes messages AFTER March 2004 is at this site. Using Freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Setting the origin in native space
External Email - Use Caution Hello FreeSurfer users, I want to use the suit software to segment the cerebellum, however the software requires the origin be set at the anterior composure. I know the Talairach image’s origin is set at the anterior commisure and that there is a Talairach transformation in mri/transforms. Is there a way to use this information to set the origin to the anterior commisure in the native space image? Thanks in advance, Ryan Nillo Staff Research Associate UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using the SUIT atlas
External Email - Use Caution Hi FreeSurfer users, I am using the SUIT atlas (http://www.diedrichsenlab.org/imaging/suit.htm) to parcellate the cerebellum.To ensure there are no problems with registration, the SUIT pipeline requires that the origin of the input images are centered at the anterior commissure. Does FreeSurfer have any tools to set this origin from the command line? Thank you for your help, Ryan Nillo Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] re-run fsaverage only
External Email - Use Caution Hello, I accidentally renamed my fsaverage directory when I was renaming my subjects' directories. Since I was still in the process of running subjects, a new fsaverage directory was automatically created. Now I have two fsaverage directories that each have a different subset of my participants, but I'd like there to be one directory that has all my participants. Is there any command that I could run that would generate a new fsaverage from subjects in the same output directory? Thanks, Ryan Wales -- Ryan Wales Graduate Student Cognition and Motor Control Neuroscience Laboratory Integrative Neuroscience Psychology Department Stony Brook University E-mail: ryan.wa...@stonybrook.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extracting values from a single vertex
External Email - Use Caution Hi FreeSurfer users, I want to extract thickness values at a single vertex. I searched on the support list and found an mris_convert command to use. However, the file I want to extract values from is a volume with multiple frames. When I try to use mris_convert on it, I only got the value at a vertex on the first frame. The goal is to set that vertex as a seed point and use the values as a regressor for glm. Is there a way to do this with FreeSurfer's commandline tools, or should I do this in Matlab? Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] automating custom color map
External Email - Use Caution Thank you so much, Ruopeng. Do you have an estimated timeline for when this option might be done? Ryan From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ruopeng Wang Sent: Thursday, November 1, 2018 7:18:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] automating custom color map I think there is no option to set custom color code for overlay from command-line. I’ll add that option and let you know when it’s ready. Best, Ruopeng On Nov 1, 2018, at 4:51 PM, Nillo, Ryan Michael R mailto:ryanmichael.ni...@ucsf.edu>> wrote: External Email - Use Caution Hi Freesurfer Users, I used linear regression to map regional beta values on the fsaverage surface. I want to use a colormap that goes from blue to gray or gray to red (no cyan and yellow). I've been using a custom colormap shown in example.tiff. I've been making this by going into freeview and adjusting the parameters from the GUI. Is there a way to load this and create a snapshot from the command line? I know you can adjust certain parameters like overlay threshold and change the colormap, but I don't see an option for "custom". The end goal is to make multiple regression models and automate the screenshot process. Best, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Research Opportunity
External Email - Use Caution UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar for The Laboratory for Precision Neuroimaging We are seeking a postdoctoral candidate with a strong background in genetics human imaging and a desire to use a multi-disciplinary approach to pursue neurodegenerative and neurodevelopment research. The candidate should have a strong statistical/computational background with experience with data analytic tools such as Matlab, R, and PLINK and potentially, MRI image analysis tools such as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree with less than five years of postdoctoral experience. Highly motivated individuals with a record of productive research are encouraged to apply. The position is available starting immediately. Salary is commensurate with qualifications and experience. Job Requirements: 1.CV/NIH biosketch (must contain previous research experience) 2.Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3.Three references If interested please contact Dr. Leo Sugrue at leo.sug...@ucsf.edu<mailto:leo.sug...@ucsf.edu> Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Designing Constrats for 3 Group 1 Covariate Analysis
External Email - Use Caution Dear freesurfers, I have what is likely a basic question but I'm new not only to FreeSurfer but contrast matrix design and group analysis as well, and was hoping for some help/clarification. Basically I want to run a GLM on our structural/functional data in order to determine if there's any significant correlation between cortical thickness and cortical amyloid deposition (measured by PiB), factoring in any potential effects of APOE genotype (e3e3, e3e4, e4e4). This means I want to construct an FSGD file with a 3 groups (the 3 APOE genotypes) and 1 covariate (our calculated cortical composite PiB value) for this analysis. However, I'm struggling with the proper contrast designs which test the various hypotheses in such a setup. Any answers, thoughts, or insights would be greatly appreciated. I know this type of analysis is also likely QDEC-able, but I think the FSGD approach would be more beneficial for my understanding of contrast matrix design. Please let me know if I've left out any information that could potentially help clarify my question/request. Best, Ryan O'Dell MD/PhD PGY2 Psychiatry Resident, NRTP Yale University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hippocampal subfield segmentation
ad_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression Started at Tue Aug 21 16:43:10 PDT 2018 Ended at Tue Aug 21 16:43:39 PDT 2018 #@#%# recon-all-run-time-hours 0.008 recon-all -s sub_0006_T1_20160920_1723 finished without error at Tue Aug 21 16:43:39 PDT 2018 done From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Tuesday, August 21, 2018 3:17:15 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation External Email - Use Caution Hi Ryan, Is it possible that you're mixing versions of FreeSurfer in your PATH and/or LD_LIBRARY_PATH? Maybe you could try unsetting them before you source FreeSurfer? Cheers, /Eugenio Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nillo, Ryan Michael R Sent: Tuesday, August 21, 2018 9:58:25 PM To: Freesurfer support list Subject: [Freesurfer] hippocampal subfield segmentation External Email - Use Caution Hello FreeSurfer users, I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a directory called MCRv80 in my FREESURFER_HOME. The first error says kvlAutoCrop: command not found. However, $FREESURFER_HOME.bin is on my path. Does anything seem incorrect? My path looks like this: /data/sugrue2/rnillo/tools:/data/sugrue2/rnillo:/netopt/afni:/working/sdl_analysis/software/dcm2niix/build/bin:/netopt/rhel7/versions/cmtk/lib/cmtk/bin:/working/sdl_analysis/software/vtk-dicom/build/bin:/netopt/dicom/bin:/working/sdl_analysis/software/ANTs/antsbin/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/mni/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/share/bin/local/sdl/fix:/netopt/rhel7/fsl/bin:/working/sdl_analysis/software/git_pipeline/CommandLineProg:/netopt/share/local/bin/sdl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/sbin:/working/sdl_analysis/software/git_unwarp:/working/sdl_analysis/software/parallel:/working/sdl_analysis/software/git_tools:/working/sdl_analysis/software/anaconda3/bin:/bin:/sbin:/usr/bin::/netopt/rhel7/bin:/netopt/rhel7/bin/local:/netopt/share/bin:/netopt/share/bin/local:/netopt/bin:/netopt/bin/local:/netopt/dicom/bin:/netopt/rhel7/matlab/bin:/netopt/ctf/bin:/netopt/share/hosts::/netopt/caret/bin:/netopt/afni:/netopt/freesurfer/bin/Linux:/netopt/freesurfer/bin/noarch:/netopt/sybase/12.5.3/OCS-12_5/bin:/netopt/rhel7/fsl/bin:/netopt/sge_n1ge6/bin/lx24-amd64:/netopt/rhel7/tivoli/tsm/client/ba/bin::/netopt/share/bin/local/sdl:/netopt/bin/local/brain:/netopt/share/bin/local/brain:/netopt/bin/local/ncl:/netopt/share/bin/local/ncl:. MatlabRuntime - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime> surfer.nmr.mgh.harvard.edu Matlab Runtime. The brainstem and hippocampal subfield modules in FreeSurfer 6.0 and the development version require the Matlab R2012b (v8.0) runtime (note that development versions from January 2018 onwards require the Matlab R2014b - v8.4 - runtime instead). ERROR MESSAGE: # #@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 13:45:25 PDT 2018 -- Setting up environment variables --- LD_LIBRARY_PATH is .:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin: Warning: Unable to open display '10.48.0.125:0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in
[Freesurfer] hippocampal subfield segmentation
ocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlApplyTransform: line 3: kvlApplyTransform.bin: command not found mv: cannot stat ‘imageDump_transformed.mgz’: No such file or directory /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_right//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Thickness measurements.
External Email - Use Caution Hello FreeSurfer experts, I want to use FreeSurfer to generate thickness files using my own surfaces. Is there a way to use white and pial surfaces not generated from the mris_make_surfaces to create thickness files? Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal Processing question
External Email - Use Caution Hello FreeSurfer experts, I have a few questions on the longitudinal processing stream. I am interested in studying longitudinal morphometry changes in a pediatric population. The age range of this population is between 4-20 years with age deltas between a few months to < 2 years. I want to know what are appropriate/acceptable age deltas used for longitudinal processing. I looked through the archives and one researcher asked about age deltas. One of the answers was that “if the time delta is relatively small, this has good chances to work”. What does “relatively small” mean? If the time points exit the longitudinal pipeline without errors and the surfaces look correct, does this mean the data is relevant?? When I correct for head size, should I use the eTIV values from the cross-sectional directories or the longitudinal directories? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit question
External Email - Use Caution Hello FreeSurfer Users, I want to run an ROI-based analysis on mri_glmfit as opposed to vertex-based. I know that if I run mri_glmfit with the --table flag and give it the output of asegstats2table or aparcstats2table, it will run the analysis on the ROIs and output tables showing significance. In each contrast directory that was created from mri_glmfit, I see there is a pcc.mgh. Is there any way to display this on the surface or put it into a table format? Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas
External Email - Use Caution
Hi again Doug,
Sorry for not realizing this earlier, but I actually found a workflow that you
created, which outlines the steps really well.
(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness)
However, instead of 'fsaverage' I used the the MNI brain I had previously
recon-ed to map the ROI to the surface. By using mri_surf2surf I mapped my
subject's thickness data to the mni brain and optained the cortical thickness.
My questions are the following: how do I obtain the surface area and volume for
this ROI? Is there a way to also obtain non-segmented stats? Also, the reason I
didn't map the ROI to fsaverage was because I didn’t have access...is there a
way to change that?
Thank you for your time.
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
On 6/14/18, 11:32 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve" wrote:
You can create an annotation with mris_seg2annot and then view it in
freeview. Run it with --help to get docs
On 06/14/2018 02:18 PM, Ryan Flores wrote:
> External Email - Use Caution
>
> Great. That seemed to have worked. Is there a way to inspect that the
ROIs have been correctly placed? Perhaps by using freeview?
>
> Best,
>
> Ryan
>
-
Ryan Flores
Clinical Research Coordinator
On 6/14/18, 11:02 AM,"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve"wrote:
The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto
the surface of the subject). Use nii.gz or mgz for the output (not
img).
On 06/14/2018 01:46 PM, Ryan Flores wrote:
> External Email - Use Caution
>
> Thank you for your response. Just to clarify, the first command
should be mri_vol2surf, correct? It appears to have worked; however, I'm not
sure what my --trgsurfval should be? I'm trying the following commands, where
mni is the subject directory for the mni brain I recon-ed and sub01 is the
subject I want to transfer the atlas to so that I can obtain the cortical
thickness.
>
> 1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh
--projfrac-max 0 1 .1 --o lh.atlas.nii.gz
> 2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz
--trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf
>
> I tried running mri_surf2surf --help, but unfortunately the examples
didn’t really apply to my case. I apologize for the potential trivial question
in advance. Thanks again for your help.
>
> Best,
>
> Ryan
>
-- Ryan Flores Clinical Research Coordinator On 6/14/18, 8:33 AM,
"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve"
wrote: You can always get info by running the
command with --help. mri_vol2vol --mov atlas.nii.gz --regheader subject
--hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz This assumes that
the atlas is in registration with the mni152 (you can test with
tkregister --mov atlas.nii.gz --s subject --regheader --reg
deleteme.dat, the two volumes should be in registration) You can take
lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an
individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM,
Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > >
I
am hoping to obtain structural information (e.g., cortical > thickness,
surface area, and volume) based on the n30r83 (aka > Hammersmith)
atlas,
which is in MNI space. The atlas differentiates > between the
hemispheres by using odd/even numbers in the labels. > > After looking
through the archives I found a potential solution, which > entails
using
the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed > the MNI
brain
to obtain the proper space; however, I’m unsure of how > exactly to
implement the commands and which flags are relevant. Any > advice would
be greatly appreciated. > > Thank you for your time. I look forward to
hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > >
Clinical
Research Coordinator > > > >
___ > Freesurfer mailing
list >Freesurfer@nmr.mgh.harvard.edu >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___ Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.
Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas
External Email - Use Caution Great. That seemed to have worked. Is there a way to inspect that the ROIs have been correctly placed? Perhaps by using freeview? Best, Ryan -- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:02 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" wrote: The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or mgz for the output (not img). On 06/14/2018 01:46 PM, Ryan Flores wrote: > External Email - Use Caution > > Thank you for your response. Just to clarify, the first command should be mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my --trgsurfval should be? I'm trying the following commands, where mni is the subject directory for the mni brain I recon-ed and sub01 is the subject I want to transfer the atlas to so that I can obtain the cortical thickness. > > 1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz > 2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf > > I tried running mri_surf2surf --help, but unfortunately the examples didn’t really apply to my case. I apologize for the potential trivial question in advance. Thanks again for your help. > > Best, > > Ryan > -- Ryan Flores Clinical Research Coordinator On 6/14/18, 8:33 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" wrote: You can always get info by running the command with --help. mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz This assumes that the atlas is in registration with the mni152 (you can test with tkregister --mov atlas.nii.gz --s subject --regheader --reg deleteme.dat, the two volumes should be in registration) You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM, Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > > I am hoping to obtain structural information (e.g., cortical > thickness, surface area, and volume) based on the n30r83 (aka > Hammersmith) atlas, which is in MNI space. The atlas differentiates > between the hemispheres by using odd/even numbers in the labels. > > After looking through the archives I found a potential solution, which > entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed > the MNI brain to obtain the proper space; however, I’m unsure of how > exactly to implement the commands and which flags are relevant. Any > advice would be greatly appreciated. > > Thank you for your time. I look forward to hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas
External Email - Use Caution
Thank you for your response. Just to clarify, the first command should be
mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my
--trgsurfval should be? I'm trying the following commands, where mni is the
subject directory for the mni brain I recon-ed and sub01 is the subject I want
to transfer the atlas to so that I can obtain the cortical thickness.
1. mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max 0 1
.1 --o lh.atlas.nii.gz
2. mri_surf2surf --srcsubject mni --srcsurfval lh.atlas.nii.gz --trgsubject
sub01 --trgsurfval hammers-01-lh.img --mapmethod nnf
I tried running mri_surf2surf --help, but unfortunately the examples didn’t
really apply to my case. I apologize for the potential trivial question in
advance. Thanks again for your help.
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
On 6/14/18, 8:33 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve" wrote:
You can always get info by running the command with --help.
mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh
--projfrac-max 0 1 .1 --o lh.atlas.nii.gz
This assumes that the atlas is in registration with the mni152 (you can
test with tkregister --mov atlas.nii.gz --s subject --regheader --reg
deleteme.dat, the two volumes should be in registration)
You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to
transfer to an individual. Make sure to use --mapmethod nnf
On 06/13/2018 06:59 PM, Ryan Flores wrote:
>
> External Email - Use Caution
>
> Hello all,
>
> I am hoping to obtain structural information (e.g., cortical
> thickness, surface area, and volume) based on the n30r83 (aka
> Hammersmith) atlas, which is in MNI space. The atlas differentiates
> between the hemispheres by using odd/even numbers in the labels.
>
> After looking through the archives I found a potential solution, which
> entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed
> the MNI brain to obtain the proper space; however, I’m unsure of how
> exactly to implement the commands and which flags are relevant. Any
> advice would be greatly appreciated.
>
> Thank you for your time. I look forward to hearing from you.
>
> Best,
>
> Ryan
>
> --
>
> Ryan Flores
>
> Clinical Research Coordinator
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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[Freesurfer] Cortical Thickness Using N30R83 Atlas
External Email - Use Caution Hello all, I am hoping to obtain structural information (e.g., cortical thickness, surface area, and volume) based on the n30r83 (aka Hammersmith) atlas, which is in MNI space. The atlas differentiates between the hemispheres by using odd/even numbers in the labels. After looking through the archives I found a potential solution, which entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed the MNI brain to obtain the proper space; however, I’m unsure of how exactly to implement the commands and which flags are relevant. Any advice would be greatly appreciated. Thank you for your time. I look forward to hearing from you. Best, Ryan -- Ryan Flores Clinical Research Coordinator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, kvlAutoCrop.bin was located there, as expected. When I tried to run the step manually, it produced the correct output, but the next step gave me the similar error: command not found. I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other binaries were there, as well. The binaries are correctly exported on my PATH. I also made sure to download the Matlab compiler runtime and made sure they were on my PATH. I am running freesurfer on a Linux machine with the RedHat 7.5 OS.Any help is greatly appreciated. Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, kvlAutoCrop.bin was located there, as expected. When I tried to run the step manually, it produced the correct output, but the next step gave me the similar error: command not found. I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other binaries were there, as well. The binaries are correctly exported on my PATH. I also made sure to download the Matlab compiler runtime and made sure they were on my PATH. Any help is greatly appreciated. Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon-all w/ Hammersmith atlas
External Email - Use Caution
Hi Doug,
I just wanted to follow up on this. Were you able to download the zip file ok?
Best,
Ryan
On 4/18/18, 10:46 AM, "Ryan Flores" <rya...@stanford.edu> wrote:
Yes, of course. Please see attached.
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
On 4/18/18, 10:39 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu> wrote:
can you send me Hammers_mith_atlas_n30r83_SPM5.nii.gz ?
On 04/17/2018 07:55 PM, Ryan Flores wrote:
>
> Hi Doug,
>
> Thank you for your response. I attempted to run recon-all on the
> Hammersmith nifti file as suggested, but unfortunately it appears to
> have run into some issues. I’ve attached the recon-all.log for
reference.
>
> Best,
>
> Ryan
>
> --
>
> Ryan Flores
>
> Clinical Research Coordinator
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
> Greve <dgr...@mgh.harvard.edu>
> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Date: *Tuesday, April 17, 2018 at 9:33 AM
> *To: *"freesurfer@nmr.mgh.harvard.edu"
<freesurfer@nmr.mgh.harvard.edu>
> *Subject: *Re: [Freesurfer] Recon-all w/ Hammersmith atlas
>
> Sorry, just seeing that you also want cortical summaries. Those might
> be easier. You should run recon-all on the T1 template for the
> hammersmith. You can then create your own hammersmith annotation by
> mapping the atlas labels onto the surface (mri_vol2surf) and then
> mris_seg2annot. You can then use mris_apply_reg to map the annotation
> to the surface of an individual (or fsaverage).
>
> On 4/16/18 3:14 PM, Ryan Flores wrote:
>
> Hi Freesurfer Developers,
>
> Our group is hoping to obtain the cortical thickness, surface
> area, and volume for various cortical regions (as well as some
> subcortical volumes); however, we would like these values to be
> outputted with respect to the regions delineated in the
> Hammersmith atlas. This atlas is available for free online
>
(http://brain-development.org/brain-atlases/adult-brain-maximum-probability-map-hammers-mith-atlas-n30r83-in-mni-space/)
> and I’ve included a screenshot to show you what files are included
> in the download. Based on this information, what is the best
> and/or most straight forward to move forward?
>
> Thank you for your time. I look forward to hearing from you.
>
> 1. FreeSurfer version:
> freesurfer-i386-apple-darwin11.4.2-stable6-20170119
> 2. Platform: macOS High Sierra (Version 10.13.1)
>
> Best,
>
> Ryan
>
> --
>
> Ryan Flores
>
> Clinical Research Coordinator
>
>
>
>
> ___
>
> Freesurfer mailing list
>
>
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
> ___
> Freesurfer mailing list
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Re: [Freesurfer] Recon-all w/ Hammersmith atlas
Hi Doug, Thank you for your response. I attempted to run recon-all on the Hammersmith nifti file as suggested, but unfortunately it appears to have run into some issues. I’ve attached the recon-all.log for reference. Best, Ryan -- Ryan Flores Clinical Research Coordinator From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, April 17, 2018 at 9:33 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all w/ Hammersmith atlas Sorry, just seeing that you also want cortical summaries. Those might be easier. You should run recon-all on the T1 template for the hammersmith. You can then create your own hammersmith annotation by mapping the atlas labels onto the surface (mri_vol2surf) and then mris_seg2annot. You can then use mris_apply_reg to map the annotation to the surface of an individual (or fsaverage). On 4/16/18 3:14 PM, Ryan Flores wrote: Hi Freesurfer Developers, Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-map-hammers-mith-atlas-n30r83-in-mni-space/) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward? Thank you for your time. I look forward to hearing from you. 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2. Platform: macOS High Sierra (Version 10.13.1) Best, Ryan -- Ryan Flores Clinical Research Coordinator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer recon-all.log Description: recon-all.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] localGI issues
/ 153692 face 7 / 153692 face 75000 / 153692 face 8 / 153692 face 85000 / 153692 face 9 / 153692 face 95000 / 153692 face 10 / 153692 face 105000 / 153692 face 11 / 153692 face 115000 / 153692 face 12 / 153692 face 125000 / 153692 face 13 / 153692 face 135000 / 153692 face 14 / 153692 face 145000 / 153692 face 15 / 153692 mesh_outer = vertices: [76848x3 double] faces: [153692x3 double] facesOfVertex: [76848x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (189.57 sec). ... creating path file for vertex 1 / 76848 area file for outer ROIs saved at 1 In an assignment A(:) = B, the number of elements in A and B must be the same. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! Linux andaman.radiology.ucsf.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Sat Sep 9 03:55:24 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub_0015 exited with ERRORS at Thu Nov 9 14:11:33 PST 2017 For more details, see the log file /data/sugrue2/NF1_qdec/sub_0015/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you for your time, Ryan Nillo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] LGI error
Hello FS users,
I am using FreeSurfer version 5.3 to calculate local verification index and
processing stopped at make_roi_paths. Here, I was given the error below. I
searched in the archives and found a solution to the problem was to edit a few
lines on SearchProjectionOnPial.m. The new script is included below the error.
Any advice on how to fix this would be greatly appreciated.
Make_roi_paths error
=
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/P0007/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_20907_.m');
exit
=
< M A T L A B (R) >
Copyright 1984-2015 The MathWorks, Inc.
R2015b (8.6.0.267246) 64-bit (glnxa64)
August 20, 2015
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com<http://www.mathworks.com>.
modified_matlab =
/working/sdl_analysis/software/freesufer_5.3_matlab
Academic License
>> loading datas ...
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done ( 0.07 sec)
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done ( 0.02 sec)
preparing outer mesh structure ...
face 5000 / 132292
face 1 / 132292
face 15000 / 132292
face 2 / 132292
face 25000 / 132292
face 3 / 132292
face 35000 / 132292
face 4 / 132292
face 45000 / 132292
face 5 / 132292
face 55000 / 132292
face 6 / 132292
face 65000 / 132292
face 7 / 132292
face 75000 / 132292
face 8 / 132292
face 85000 / 132292
face 9 / 132292
face 95000 / 132292
face 10 / 132292
face 105000 / 132292
face 11 / 132292
face 115000 / 132292
face 12 / 132292
face 125000 / 132292
face 13 / 132292
mesh_outer =
vertices: [66148x3 double]
faces: [132292x3 double]
facesOfVertex: [66148x1 struct]
preparing pial mesh structure ...
...searching for mesh edges...done (140.10 sec).
... creating path file for vertex 1 / 66148
area file for outer ROIs saved at 1
In an assignment A(:) = B, the number of elements in A and B must be the same.
Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));
Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);
Error in reorganize_verticeslist (line 28)
[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);
SearchProjectionOnPial.m Script
function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim,
step)
% step is typically set between 5 and 10. Default is 7, increasing it will
% limit redundancies in the resulting path file.
verticeslist=[];
si=max(size(perim));
for t=1:step:si
[nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:));
verticeslist= [verticeslist nearestIndexMT];
end
verticeslist=unique(verticeslist);
Sincerely,
Ryan Nillo
UCSF Center for Radiology and Biomedical Imaging
Staff Research Associate
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Re: [Freesurfer] mri_glmfit mask.mgh for mri_surfcluster
Perfect --- Thank you! Ryan > On May 15, 2017, at 6:09 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > usually the fsaverage mask is fine. You can use mri_label2label with the > --outmask option to convert the ?h.cortex.label to a binary mask. You > can also pass surfcluster a label directly with the --clabel option > > > On 05/14/2017 05:45 AM, Ryan Muetzel wrote: >> Dear Experts, >> >> This is partially a follow-up question to another thread related to >> the mask.mgh generated by mri_glmfit >> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html). >> >> We would like to use the mri_surfcluster tool on a log10p map. I’m >> wondering — for vertex-wise analyses that use freesurfer-specific >> output (e.g., thickness, surface area, lgi, etc, not FMRI or DTI >> data)….can we rely on a single mask image for each hemisphere that >> comes from the fsaverage ?h.cortex.label? Or, should we be creating a >> mask that is specific to a given analysis/dataset, as is done with >> mri_glmfit? >> >> If the latter, is there a way to create this mask outside of mri_glmfit? >> >> Thank you in advance for your time and help! >> >> Best, >> >> Ryan >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit mask.mgh for mri_surfcluster
Dear Experts, This is partially a follow-up question to another thread related to the mask.mgh generated by mri_glmfit (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html>). We would like to use the mri_surfcluster tool on a log10p map. I’m wondering — for vertex-wise analyses that use freesurfer-specific output (e.g., thickness, surface area, lgi, etc, not FMRI or DTI data)….can we rely on a single mask image for each hemisphere that comes from the fsaverage ?h.cortex.label? Or, should we be creating a mask that is specific to a given analysis/dataset, as is done with mri_glmfit? If the latter, is there a way to create this mask outside of mri_glmfit? Thank you in advance for your time and help! Best, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] -hemi flag
Hi FreeSurfer users, I am using FreeSurfer v5.3 and have noticed that when -hemi is used as a flag in recon-all, the half I did not specify is not present in wm.mgz. The full command is recon-all -autorecon2 -autorecon3 -hemi (l or r)h -subjid subject_name -sd SUBJECTS_DIR. After running, white matter is missing in the half of wm.mgz not specified under the -hemi flag, but the surfaces and segmentation in aparc+aseg are unaffected. Is this a bug? Ryan Michael Nillo UCSF Center for Radiology and Biomedical Imaging Staff Research Associate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] v6 Hippocampal subfields on a cluster
Dear Experts, I am trying to run the Hippocampal and brainstem MCR code on a cluster. When I schedule a job with anywhere between 2-4GB of RAM per dataset (i.e., per core), I am getting both java and matlab errors (from java, it is a GC out of memory error, and from matlab it is a vague segmentation fault). If I schedule the job with 6+GB of RAM, things run just fine. My sense is that there are maybe some multi-core/thread or memory settings in either java or the MCR that are causing trouble here? Or does this process really need 6GB of RAM? If the RAM requirements are closer to the 2-3GB range, do you happen to know of any flags I can/should pass to java/MCR to limit the parallel/memory expectations? For example, I’ve tried: export _JAVA_OPTIONS="-XX:ParallelGCThreads=1”, but without any luck. Let me know if you have any suggestions! Al the best, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error loading surface on one machine, but not another
Hi All I created surfaces for a particular subject on one machine, and subsequently copied the entire subjects surface directory to another machine (both running OSX, although different versions). On the second machine, I cannot load the lh surfaces files. For example % tksurfer LS lh white produces the following output and error (last line): tksurfer LS lh white subject is LS hemiis lh surface is white surfer: current subjects dir: /Users/rmruczek/MR_DATA/surfaces surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/rmruczek/MR_DATA/surfaces/LS/surf checking for nofix files in 'white' Reading image info (/Users/rmruczek/MR_DATA/surfaces/LS) Reading /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz surfer: Reading header info from /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz mrisFindNeighbors: /Users/rmruczek/MR_DATA/surfaces/LS/surf/lh.white: face[0].v[0] = 0, but face 0 not in vertex 0 face list This is a problem for all of the left hemisphere surfaces on the new machine. The same command executes fine on the original machine. Also, the right hemisphere surfaces load fine on the second machine. I've double checked that the files were copied completely and were not truncated. Has anyone experienced something similar or have an idea of what is going on? Thanks! Cheers, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error loading surface on one machine, but not another
Yes, and they indeed do not match up on the two machines. I transferred twice, not sure why there would be this issue with just the lh files. I changed ftp programs and that seems to work. Thanks for pointing me toward in the (now) obvious route of doing the checksums. Cheers, Ryan On Dec 13, 2013, at 6:33 PM, Bruce Fischl wrote: can you checksum the files on both machines? On Fri, 13 Dec 2013, Ryan Mruczek wrote: Hi All I created surfaces for a particular subject on one machine, and subsequently copied the entire subjects surface directory to another machine (both running OSX, although different versions). On the second machine, I cannot load the lh surfaces files. For example % tksurfer LS lh white produces the following output and error (last line): tksurfer LS lh white subject is LS hemiis lh surface is white surfer: current subjects dir: /Users/rmruczek/MR_DATA/surfaces surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/rmruczek/MR_DATA/surfaces/LS/surf checking for nofix files in 'white' Reading image info (/Users/rmruczek/MR_DATA/surfaces/LS) Reading /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz surfer: Reading header info from /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz mrisFindNeighbors: /Users/rmruczek/MR_DATA/surfaces/LS/surf/lh.white: face[0].v[0] = 0, but face 0 not in vertex 0 face list This is a problem for all of the left hemisphere surfaces on the new machine. The same command executes fine on the original machine. Also, the right hemisphere surfaces load fine on the second machine. I've double checked that the files were copied completely and were not truncated. Has anyone experienced something similar or have an idea of what is going on? Thanks! Cheers, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] localGI Matlab runtime?
Hello, I was wondering if anyone has compiled the localGI code with the matlab runtime integrated with recon-all? We have a lot of data that we'd like to run through the localGI stream, however we have a limited number of matlab licenses. Are there other easy ways to parallelize this (i.e., run different subjects on different cores) without using up many matlab licenses? Thank you! All the best, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Optseq2 design question - series of events
Hi all - I'm trying to design my first event related experiment, and I'm having trouble figuring out how to best optimize the design...wondering if you have any insights: I have two conditions (milkshake and water). Each condition has several events in order: Participants get a squirt of milkshake (4s) then swallow (jittered?) then a rinse of water (no interest) then swallow (jitter again?). In the other condition, they just get a squirt of water and a swallow. In order to model all of this, would I need to put in every event that's taking up time as an event, and then just do an event contrast comparing the two conditions of interest (receipt of milkshake/water)? Or would I make the events be long enough to encompass all the actions that are taking place during that event (even though I'm just interested in the first 4s when the person is receiving a taste)? thanks for any tips. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Training Comparison
Hello all, I'm doing a training comparison (training type A vs. type B), and I created thickness difference files (the rate files from the long_mris_slopes command) for each subject. How can I conduct an FSGD analysis with these thickness difference files? I tried replacing all of the lh.thickness and rh.thickness files with the lh.long.thickness-rate files, but it gives me the following error: MRISreadBinaryCurvature: incompatible vertex number in file /Applications/freesurfer/subjects/7107-60_base/surf/lh.thickness ERROR: reading curvature file -- -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] (no subject)
Doug, I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd fsgd doss --C training-effect.mtx On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: On 11/01/2012 06:35 PM, Ryan wrote: Doug, Picture 4 shows the difference between the medial surface for this analysis and for another type of analysis (where I created my own matrix file) that completed normally. Is this normal? I have never looked at this surface for errors before, which is why I ask. That is normal. Usually, the medial wall is masked out. Picture 5 shows the command you just requested I run, and all points across the cortical mantle look like this image - nothing seems to be at exactly the same level. That looks normal. What is your mri_glmfit command-line? Not the mri_glmfit-sim cmd line. On Thu, Nov 1, 2012 at 5:55 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: The mask looks ok to me (I did not notice anything strange around the CC). How do the sig maps look? Is there any data set in there that is odd? you can evaluate this with tksurfer fsaverage lh inflated -ov glmdir/mask.mgh -fminmax .5 1-t y.mgh this will bring up a time course where each point is an input. See if there are any inputs that are always 0 or some other outlier. doug On 11/01/2012 04:50 PM, Ryan wrote: Doug, I attached the tksurfer images that I get with your command, the area around the corpus callosum is oddly yellow. What caused this mask problem, and how can I fix it? Thanks. On Thu, Nov 1, 2012 at 2:55 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: The problem is that the fwhm is not-a-number (glmdir/fwhm.dat). Usually this means that there is something messed up with the mask (glmdir/mask.mgh). View the mask to see what is up tksurfer fsaverage lh inflated -ov glmdir/mask.mgh -fminmax .5 1 doug On 11/01/2012 02:39 PM, Ryan wrote: Doug, Here are the files. On Thu, Nov 1, 2012 at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Can you send the command line and attach the files? thanks doug On 11/01/2012 01:11 PM, Ryan wrote: Doug, I tried running mri_glmfit-sim without the --bg flag and it finished in 10 minutes without any errors. This has never happened before, so I highly suspect these results. Do you know what could be wrong? In case you need it, the summary file output and terminal output are attached. -Ryan -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki
Re: [Freesurfer] (no subject)
Doug, The analysis has been running for about 45 minutes, but I'll e-mail you if there are any more errors. Thank you. On Fri, Nov 2, 2012 at 12:41 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: If this is a surface based analysis, then you'll need to add --surface fsaverage rh doug On 11/02/2012 11:34 AM, Ryan wrote: Doug, I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd fsgd doss --C training-effect.mtx On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: On 11/01/2012 06:35 PM, Ryan wrote: Doug, Picture 4 shows the difference between the medial surface for this analysis and for another type of analysis (where I created my own matrix file) that completed normally. Is this normal? I have never looked at this surface for errors before, which is why I ask. That is normal. Usually, the medial wall is masked out. Picture 5 shows the command you just requested I run, and all points across the cortical mantle look like this image - nothing seems to be at exactly the same level. That looks normal. What is your mri_glmfit command-line? Not the mri_glmfit-sim cmd line. On Thu, Nov 1, 2012 at 5:55 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: The mask looks ok to me (I did not notice anything strange around the CC). How do the sig maps look? Is there any data set in there that is odd? you can evaluate this with tksurfer fsaverage lh inflated -ov glmdir/mask.mgh -fminmax .5 1-t y.mgh this will bring up a time course where each point is an input. See if there are any inputs that are always 0 or some other outlier. doug On 11/01/2012 04:50 PM, Ryan wrote: Doug, I attached the tksurfer images that I get with your command, the area around the corpus callosum is oddly yellow. What caused this mask problem, and how can I fix it? Thanks. On Thu, Nov 1, 2012 at 2:55 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: The problem is that the fwhm is not-a-number (glmdir/fwhm.dat). Usually this means that there is something messed up with the mask (glmdir/mask.mgh). View the mask to see what is up tksurfer fsaverage lh inflated -ov glmdir/mask.mgh -fminmax .5 1 doug On 11/01/2012 02:39 PM, Ryan wrote: Doug, Here are the files. On Thu, Nov 1, 2012 at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: Can you send the command line and attach the files? thanks doug
Re: [Freesurfer] (no subject)
Doug, I tried running mri_glmfit-sim without the --bg flag and it finished in 10 minutes without any errors. This has never happened before, so I highly suspect these results. Do you know what could be wrong? In case you need it, the summary file output and terminal output are attached. -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] (no subject)
Doug, Here are the files. On Thu, Nov 1, 2012 at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you send the command line and attach the files? thanks doug On 11/01/2012 01:11 PM, Ryan wrote: Doug, I tried running mri_glmfit-sim without the --bg flag and it finished in 10 minutes without any errors. This has never happened before, so I highly suspect these results. Do you know what could be wrong? In case you need it, the summary file output and terminal output are attached. -Ryan -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -Ryan terminal Description: Binary data summary Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Files
Doug, Just so our study is understandable, subjects completed a 6 week period of training or no training (i.e. the control condition) with a scan at the beginning and end of the period. Thus, I entered the pre and post-scans for training and control subjects in the input files. The names for all the subjects are kept in an ordered list, referenced by the other two files I describe below. In the Xg.dat file, the first column has a +1 for each control subject's pre-scan and a -1 for each control subject's post-scan. The second column has a +1 for each training subject's pre-scan and a -1 for each training subject's post-scan. The remaining columns each pertain to a specific subject's two scans, with 1's showing FreeSurfer which two scans are being compared pre to post. In the mtx file, the -1 references the first column in Xg.dat (control subjects) and the +1 references the second column in Xg.dat (training subjects). The remaining 0's refer to the other subjects or columns in Xg.dat. So in order to determine whether there's thickening or thinning in the controls and training subjects, would I still need to use an additional analysis with the contrasts [1 0 0 ] and [0 1 0 ]? Thank you. On Tue, Oct 30, 2012 at 11:28 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Ryan, I'm a little lost here. Can you resend your X and contrast matrices and explain what each column is? doug On 10/26/2012 03:45 PM, Ryan wrote: Doug, Actually my input is not the difference map, but the separate time points (it's timepoint 2 weighted with -1 and timepoint 1 weighted with 1, described in the matrix file I sent you). So in order to determine whether there's thickening or thinning in the controls and training subjects, would I still need to use the additional contrasts [1 0 0 ] and [0 1 0 ]? Thank you. On Thu, Oct 25, 2012 at 3:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: And the input is already TimePoint2-TimePoint1? If so, then you will need two more contrasts: [1 0 0 ] and [0 1 0 ]. The first tells you if controls are thinning (blue) or thickening (red), the 2nd tells you if the training is doing the same. doug On 10/25/2012 03:34 PM, Ryan wrote: Doug, Yes, it's a longitudinal study since we MRI participants pre-training and post-training. On Thu, Oct 25, 2012 at 2:37 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: I'm not sure I understand. Is this a longitudinal study? On 10/25/2012 01:26 PM, Ryan wrote: Doug, Also, how can I tell if it's thickening or thinning if red/blue corresponds to the group? Thanks for the help. -- Forwarded message -- From: *Douglas N Greve* gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Date: Thu, Oct 25, 2012 at 12:20 PM Subject: Re: Files To: Ryan wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu That contrast will compute training-controls. In the maps, red/yellow will mean trainingcontrols, blue/cyan otherwise doug On 10/25/2012 12:47 AM, Ryan wrote: Doug, Here are the Xg.dat (where the first column is for controls and the second column is for training subjects) and mtx files, I didn't use the FSGD design. Please let me know if this is sufficient for you to answer my question, thank you very much. ---Ryan -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr
Re: [Freesurfer] Files
Doug, So if I wanted to test if there were effects of training compared to the control condition, and I had 4 subjects (2 per group), would the format for my two files shown below be correct? Thanks. FSGD file: GroupDescriptorFile 1 Class Subject1 Class Subject2 Class Subject3 Class Subject4 Variables TP1-vs-TP2.Group1Train TP1-vs-TP2.Group2Control Input 1-2_recon Subject1 1 0 Input 1-3_recon Subject1 1 0 Input 2-2_recon Subject2 1 0 Input 2-3_recon Subject2 1 0 Input 3-1_recon Subject3 0 -1 Input 3-2_recon Subject3 0 -1 Input 4-1_recon Subject4 0 -1 Input 4-2_recon Subject4 0 -1 Mtx file: 0 0 0 0 1 0 0 0 0 0 0 -1 Additional Mtx file examining cortical thinning or thickening in the training group: 0 0 0 0 1 0 On Tue, Oct 30, 2012 at 4:44 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: See http://surfer.nmr.mgh.harvard.**edu/fswiki/**RepeatedMeasuresAnovahttp://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova This is for a single group. For two groups with 3 time points. In your case, you only have 2 time points (so no TP1-vs-TP3 variable). To account for the 2nd group, create two variables: TP1-vs-TP2.Group1 and TP1-vs-TP2.Group2. If a subject is in Group1, then set the Group2 variable to 0. doug On 10/30/2012 04:38 PM, Maren Strenziok wrote: If you don't agree with our matrix and contrasts, can you please send us a matrix example for a 2x2 within and between subjects ANOVA model and contrasts to get the interaction effect? Maren On Oct 30, 2012, at 4:22 PM, Douglas N Grevegr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Hi Ryan, I don't understand your model. This does not look like a standard repeated measures ANOVA. Is it supposed to be equivalent? doug On 10/30/2012 02:07 PM, Ryan wrote: Doug, Just so our study is understandable, subjects completed a 6 week period of training or no training (i.e. the control condition) with a scan at the beginning and end of the period. Thus, I entered the pre and post-scans for training and control subjects in the input files. The names for all the subjects are kept in an ordered list, referenced by the other two files I describe below. In the Xg.dat file, the first column has a +1 for each control subject's pre-scan and a -1 for each control subject's post-scan. The second column has a +1 for each training subject's pre-scan and a -1 for each training subject's post-scan. The remaining columns each pertain to a specific subject's two scans, with 1's showing FreeSurfer which two scans are being compared pre to post. In the mtx file, the -1 references the first column in Xg.dat (control subjects) and the +1 references the second column in Xg.dat (training subjects). The remaining 0's refer to the other subjects or columns in Xg.dat. So in order to determine whether there's thickening or thinning in the controls and training subjects, would I still need to use an additional analysis with the contrasts [1 0 0 ] and [0 1 0 ]? Thank you. On Tue, Oct 30, 2012 at 11:28 AM, Douglas N Greve gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.**harvard.edu gr...@nmr.mgh.harvard.edu wrote: Hi Ryan, I'm a little lost here. Can you resend your X and contrast matrices and explain what each column is? doug On 10/26/2012 03:45 PM, Ryan wrote: Doug, Actually my input is not the difference map, but the separate time points (it's timepoint 2 weighted with -1 and timepoint 1 weighted with 1, described in the matrix file I sent you). So in order to determine whether there's thickening or thinning in the controls and training subjects, would I still need to use the additional contrasts [1 0 0 ] and [0 1 0 ]? Thank you. On Thu, Oct 25, 2012 at 3:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu**mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: And the input is already TimePoint2-TimePoint1? If so, then you will need two more contrasts: [1 0 0 ] and [0 1 0 ]. The first tells you if controls are thinning (blue) or thickening (red), the 2nd tells you if the training is doing the same. doug On 10/25/2012 03:34 PM, Ryan wrote: Doug, Yes, it's a longitudinal study since we MRI participants pre-training and post-training. On Thu, Oct 25, 2012 at 2
Re: [Freesurfer] Files
Doug, Actually my input is not the difference map, but the separate time points (it's timepoint 2 weighted with -1 and timepoint 1 weighted with 1, described in the matrix file I sent you). So in order to determine whether there's thickening or thinning in the controls and training subjects, would I still need to use the additional contrasts [1 0 0 ] and [0 1 0 ]? Thank you. On Thu, Oct 25, 2012 at 3:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: And the input is already TimePoint2-TimePoint1? If so, then you will need two more contrasts: [1 0 0 ] and [0 1 0 ]. The first tells you if controls are thinning (blue) or thickening (red), the 2nd tells you if the training is doing the same. doug On 10/25/2012 03:34 PM, Ryan wrote: Doug, Yes, it's a longitudinal study since we MRI participants pre-training and post-training. On Thu, Oct 25, 2012 at 2:37 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: I'm not sure I understand. Is this a longitudinal study? On 10/25/2012 01:26 PM, Ryan wrote: Doug, Also, how can I tell if it's thickening or thinning if red/blue corresponds to the group? Thanks for the help. -- Forwarded message -- From: *Douglas N Greve* gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Date: Thu, Oct 25, 2012 at 12:20 PM Subject: Re: Files To: Ryan wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu mailto:wmcga...@gmu.edu That contrast will compute training-controls. In the maps, red/yellow will mean trainingcontrols, blue/cyan otherwise doug On 10/25/2012 12:47 AM, Ryan wrote: Doug, Here are the Xg.dat (where the first column is for controls and the second column is for training subjects) and mtx files, I didn't use the FSGD design. Please let me know if this is sufficient for you to answer my question, thank you very much. ---Ryan -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ---Ryan -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- -Ryan -- Douglas N. Greve
[Freesurfer] Training-Control Group Comparison Analysis
Hello everyone, I'm conducting an analysis involving a training group and a control group, where each group has a pre and a post scan. I setup the matrix file, the contrast file, and ran mri_glmfit along with mri_glmfit-sim for the cluster correction. The analysis finished revealing a significant cluster, although I want to confirm that my interpretation of the results is correct. I see a significant cluster which I believe means the training group showed greater thickening compared to the controls, is this correct? Also, how can I tell if clusters represent thickening or thinning in the training group compared to the control group? When I setup the matrix file, I entered 1's and -1's for the control subjects in the first column, and training subjects in the second column. When I setup the contrast file, I entered a -1 and then a 1, with 0's for the rest of the variables. Thanks for the help. -W. Ryan McGarry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Comparing cortical thickness for 2 groups
Hello everyone, I'm analyzing the data for a training study looking to see if there are changes in cortical thickness as a result of training. We have pre and post scans (training) and control subjects (no training). How do I setup this design in the Xg.dat and matrix files so I can run mri_glmfit? Thank you. Best, -W. Ryan McGarry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] (no subject)
Hello all, I'm analyzing the data for a training study our research group conducted, and I'm looking to see if there are changes in cortical thickness as a result of training. We have pre- and post-training scans, so I followed the longitudinal tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#InspectingLongitudinalData). There are 4 measures listed on the website (average, rate, pc1, and spc) - which do I choose if I simply want to see if there is a difference in cortical thickness for pre vs. post? Also, do I need to run anything afterwards such as cluster corrections? Best, -W. Ryan McGarry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] (no subject)
Hello, I'm conducting a longitudinal analysis and encounter an error when running the long_mris_slopes command (this is contained in the online tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial). The error that arises within a minute is ERROR -10 : mris_calc compute sym. pct. change (spc) problem?, any thoughts? Thanks all. -- -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] (no subject)
Hello all, I'm encountering a problem when I try to compare two timepoints for a particular subject. I run the command recon-all -all -s 7107-46-tp1 -i 7107-46-1/001.mgz and the end of the output stream where I receive errors shows the following below. Any help is greatly appreciated! painting output onto subject 7107-46-tp1. processing subject lh.EC_average... MRISread(/media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.r$ Too many levels of symbolic links Linux mriserver.archlab 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 7107-46-tp1 exited with ERRORS at Sat Feb 25 02:34:14 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] repost: error using recon-all function
Freesurfer Experts, I am reposting an error message that I receive when using the recon-all function to analyze my own data. The command which I am trying to execute is: recon-all -s 2645166 -all 2645166 is the patient ID. Running this gives an error: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2645166 exited with ERRORS at Wed Jul 6 14:06:34 CDT 2011 bugr gives this: - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 - I apologize to keep asking the same questions, but until this is resolved, I am unable to process the new data obtained in my lab. I am relatively new to using this software, so any guidance would be much appreciated! Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error using recon-all function
Freesurfer experts, I emailed last week with an error using recon-all. This problem has still not been resolved. The summary of the problem should be shown below: Thanks, Ryan On Fri, Jul 1, 2011 at 2:06 PM, Ryan Hutten ryanhutten2...@u.northwestern.edu wrote: -- Forwarded message -- From: Ryan Hutten ryanhutten2...@u.northwestern.edu Date: Thu, Jun 30, 2011 at 1:34 PM Subject: Re: [Freesurfer] error using recon-all function To: Krish Subramaniam kr...@nmr.mgh.harvard.edu Krish, under the $FREESURFER_HOME/bin directory, there is a file named avi2talxfm I copied the output of the command you sent me. tar -ztvf freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz | grep avi2tal -rwxr-xr-x root/root 2087 2011-05-22 08:28 freesurfer/bin/avi2talxfm It looks like the file is there, but something is not working with it. Any ideas? Thanks, Ryan On Thu, Jun 30, 2011 at 12:53 PM, Krish Subramaniam kr...@nmr.mgh.harvard.edu wrote: Hi Ryan We do bundle avi2talxfm in our distribution. Can you see that in $FREESURFER_HOME/bin ? If you have the original freesurfer download file.. can you do a tar -ztvf freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0.tar.gz | grep avi2tal and see if it can find in the distribution ? Krish On 06/30/2011 01:35 PM, Bruce Fischl wrote: I assume you have to install it. Nick or Krish? On Thu, 30 Jun 2011, Ryan Hutten wrote: Is this something that I can add manually to one of the files? Please let me know what steps I can take to correct this problem. Thanks, Ryan On Wed, Jun 29, 2011 at 1:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Nick: it looks like he's missing this command: tail ~/talairach_avi.log Reading: /usr/local/freesurfer/average/** 711-2C_as_mni_average_305.**4dfp.ifh Writing: talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt start time Wed Jun 29 13:05:58 CDT 2011 end time Wed Jun 29 13:06:19 CDT 2011 mpr2mni305 success avi2talxfm orig.mgz /usr/local/freesurfer/average/**mni305.cor.mgz talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt transforms/talairach.auto.xfm avi2talxfm: Command not found. On Wed, 29 Jun 2011, Ryan Hutten wrote: I have attached the talairach_avi.log file. Thanks, Ryan On Wed, Jun 29, 2011 at 1:18 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ryan, what is in transforms/talairach_avi.log? cheers Bruce On Wed, 29 Jun 2011, Ryan Hutten wrote: Hi, I am currently trying to use the recon-all function. It works fine on an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is located in a folder called 2645166 as shown in the following command. When I run the command: recon-all -s 2645166 -all I get the following error after the script runs for about a minute: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The output of your bugr script gives: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 A brief internet search found nothing regarding this avi2talxfm function. Any suggestions and/or help would be greatly appreciated. Thanks, __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error using recon-all function
Hi, I am currently trying to use the recon-all function. It works fine on an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is located in a folder called 2645166 as shown in the following command. When I run the command: recon-all -s 2645166 -all I get the following error after the script runs for about a minute: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The output of your bugr script gives: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 A brief internet search found nothing regarding this avi2talxfm function. Any suggestions and/or help would be greatly appreciated. Thanks, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] uniform sampling of the sphere
Hello, I was wondering if there was a way to uniformly parcellate the sphere into n regions, and ultimately apply this parcellation to the volume/native space to generate ROIs? Or perhaps output uniformly sampled sphere coordinates that could be converted to voxel coordinates? Thanks in advance! Ryan Muetzel University of Minnesota ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] DTI group analysis
Hello all, In trying to perform a group analysis on volumetric and DTI data (with test4d.nii.gz file created by fslmerge), I encounter an error. Any help is greatly appreciated. Also, can anyone tell me what programs they prefer to use for DTI group analysis? It seems QDEC isn't helpful if you need volumetric analyses. bash-3.2$ mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir gdfReadHeader: reading /Applications/freesurfer2/subjects/glm/gender_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 64.2 Class Means of each Continuous Variable 1 gender_male 52.5000 2 gender_female 72. INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.138.2.3 2008/08/27 13:33:05 greve Exp $ cwd /Applications/freesurfer2/subjects/4964-59 cmdline mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir sysname Darwin hostname ryan-mcgarrys-mac-pro.local machine i386 user ryanmcgarry FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Applications/freesurfer2/subjects/4964-59/test4d.nii.gz logyflag 0 usedti 0 FSGD /Applications/freesurfer2/subjects/glm/gender_age.fsgd glmdir lh.gender_age.glmdir DoFFx 0 Creating output directory lh.gender_age.glmdir Loading y from /Applications/freesurfer2/subjects/4964-59/test4d.nii.gz Matrix condition is 1765.88 Pruning voxels by frame. Found 279419 voxels in mask Saving mask to lh.gender_age.glmdir/mask.mgh search space = 2.23535e+06 ERROR: dimension mismatch between y and X. y has 2 inputs, X has 5 rows. I also ran bugr and the following output was produced: FREESURFER_HOME: /Applications/freesurfer3 Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] DTI group analysis
Hello all, In trying to perform a group analysis on volumetric and DTI data (with test4d.nii.gz file created by fslmerge), I encounter an error. Any help is greatly appreciated. Also, can anyone tell me what programs they prefer to use for DTI group analysis? It seems QDEC isn't helpful if you need volumetric analyses. bash-3.2$ mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir gdfReadHeader: reading /Applications/freesurfer2/subjects/glm/gender_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 64.2 Class Means of each Continuous Variable 1 gender_male 52.5000 2 gender_female 72. INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.138.2.3 2008/08/27 13:33:05 greve Exp $ cwd /Applications/freesurfer2/subjects/4964-59 cmdline mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir sysname Darwin hostname ryan-mcgarrys-mac-pro.local machine i386 user ryanmcgarry FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Applications/freesurfer2/subjects/4964-59/test4d.nii.gz logyflag 0 usedti 0 FSGD /Applications/freesurfer2/subjects/glm/gender_age.fsgd glmdir lh.gender_age.glmdir DoFFx 0 Creating output directory lh.gender_age.glmdir Loading y from /Applications/freesurfer2/subjects/4964-59/test4d.nii.gz Matrix condition is 1765.88 Pruning voxels by frame. Found 279419 voxels in mask Saving mask to lh.gender_age.glmdir/mask.mgh search space = 2.23535e+06 ERROR: dimension mismatch between y and X. y has 2 inputs, X has 5 rows. I also ran bugr and the following output was produced: FREESURFER_HOME: /Applications/freesurfer3 Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] DTI Analysis
Hello all, I'm doing a volumetric group analysis of DTI data and am now stuck. I ran mri_preproc, mri_info, and mri_glmfit to create sig.mgh. I run the following command and load sig.mgh as an overlay: tkmedit fsaverage brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white I'm wondering if this is the correct usage for the sig.mgh file, and if someone could point me in the right direction for what steps are next? Thank you. -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?
Thanks for your help, Nick and Bruce. I'm trying to regenerate this volume in order to verify that this is, in fact, an older bug that has been resolved in FS4. I'm assuming that by the last (fast) steps, you meant aparc2aseg and wmparc, so I used this command line: recon-all -s 2368-004-01 -aparc2aseg -wmparc aparc_fix.txt However, I keep getting this error (I included a little bit before the error just to give an idea of where it was at in the aparc2aseg process): Loading rh annotations from /Autism/autism/longitudinal/2368-004/2368-004-01/FreeSurfer/2368-004-01/label/rh.aparc.annot Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Autism/autism/longitudinal/2368-004/2368-004-01/FreeSurfer/2368-004-01/mri/ribbon.mgz ERROR: cannot find /Autism/autism/longitudinal/2368-004/2368-004-01/FreeSurfer/2368-004-01/mri/ribbon.mgz ERROR: loading /Autism/autism/longitudinal/2368-004/2368-004-01/FreeSurfer/2368-004-01/mri/ribbon.mgz Linux gaea.ia.unc.edu 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Mar 30 10:31:11 EDT 2009 Any idea of what's going on here? I find it perplexing that it's searching for a ribbon.mgz rather than an ?h.ribbon.mgz, since I found no evidence on the wiki of a file just called ribbon.mgz Ryan On Fri, Mar 27, 2009 at 4:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: yes, the thickness is independent of these. I think the only issue are the spots in the aparc+aseg, which I think we've fixed. You should be able to just rerun the very last (Fast) steps to regenerate them. cheers, Bruce On Fri, 27 Mar 2009, Ryan Scotton wrote: Hi guys, Does this mean that the measurements are probably solid, but the aparc+aseg.mgz volume inaccurately represents these measurements, or will I need to recompute the last two steps (aparc2aseg and wmparc) in order to attain accurate cortical thickness values? It doesn't like that way, since the thickness files are generated earlier in the recon stream. I ask this because we are trying to get the stats as fast as possible without having to rerun all of our cases (200+) over again. Ryan -- Forwarded message -- From: Bruce Fischl fis...@nmr.mgh.harvard.edu Date: Fri, Mar 27, 2009 at 2:47 PM Subject: Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume? To: Nick Schmansky ni...@nmr.mgh.harvard.edu Cc: Ryan Scotton ryan.scot...@gmail.com, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Hi Ryan, I think a lot of the spottyness you are seeing is a bug in FS3 that was fixed. Try using the new FS to just regenerate the aparc+aseg and see if it looks better. Bruce On Fri, 27 Mar 2009, Nick Schmansky wrote: Ryan, Be sure to have a look at ribbon.mgz, as that is a volume file created using the white and pial surfaces (from mris_volmask), and would be the most accurate of the volume files in regards to gm segmentation. Nick On Fri, 2009-03-27 at 10:53 -0400, Ryan Scotton wrote: Hi Bruce, I've uploaded an example of a case with fairly accurate white and pial boundries when viewed on top of the wm.mgz volume, and GM areas that are not segmented and others which have a very fuzzy/noisy boundary within the aparc+aseg.mgz volume. Also, I'm not sure what email client you're using, but since my first email failed to come through, I ended up forwarding it and sending it to you again yesterday, which is the one you received. I noticed that in gmail, it will hide the quoted text, which contained my best description of the problems we're seeing and my FS version (3.0.4). You may have already read it, I'm not sure, but just in case, it's inline with this email. The file I uploaded is named 5008-003-02_scotton.tar.gz Thanks so much for your help, Ryan On Thu, Mar 26, 2009 at 5:36 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ryan, I still don't quite understand what I'm looking at. Maybe you can put a problem subject somewhere we can get to it? cheers, Bruce On Thu, 26 Mar 2009, Ryan Scotton wrote: For whatever reason, my email from this morning doesn't seem to have gone through. Hopefully it will work this time... Ryan -- Forwarded message -- From: Ryan Scotton ryan.scot...@gmail.com Date: Thu, Mar 26, 2009 at 10:25 AM Subject: Re: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume? To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Hello again Bruce, We used FreeSurfer version 3.0.4, so an older version. I've attached 9 screen shots
Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?
Hi Bruce, I've uploaded an example of a case with fairly accurate white and pial boundries when viewed on top of the wm.mgz volume, and GM areas that are not segmented and others which have a very fuzzy/noisy boundary within the aparc+aseg.mgz volume. Also, I'm not sure what email client you're using, but since my first email failed to come through, I ended up forwarding it and sending it to you again yesterday, which is the one you received. I noticed that in gmail, it will hide the quoted text, which contained my best description of the problems we're seeing and my FS version (3.0.4). You may have already read it, I'm not sure, but just in case, it's inline with this email. The file I uploaded is named 5008-003-02_scotton.tar.gz Thanks so much for your help, Ryan On Thu, Mar 26, 2009 at 5:36 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ryan, I still don't quite understand what I'm looking at. Maybe you can put a problem subject somewhere we can get to it? cheers, Bruce On Thu, 26 Mar 2009, Ryan Scotton wrote: For whatever reason, my email from this morning doesn't seem to have gone through. Hopefully it will work this time... Ryan -- Forwarded message -- From: Ryan Scotton ryan.scot...@gmail.com Date: Thu, Mar 26, 2009 at 10:25 AM Subject: Re: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume? To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Hello again Bruce, We used FreeSurfer version 3.0.4, so an older version. I've attached 9 screen shots...the first 6 are from the same subject, and the last three (the jpgs with _2 at the end of them) were included just to give a better idea of the problems we're seeing in the aparc+aseg.mgz volume, despite good surfaces in the wm.mgz volume (screenshots of the wm.mgz were not included for the 2nd volume...they are equally accurate as the first case I sent). You'll notice that there are many GM areas that are not segmented and others which have a very fuzzy/noisy boundary. Do you think that there is some kind of error occuring in the spherical registration step? If so, how can one QC this step? Or is it some other issue entirely? Thanks for your help, Ryan On Tue, Mar 24, 2009 at 5:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ryan, what version are you using? And when you say bad what exactly do you mean? Can you send some snapshots? If you're doing a thickness study the aparc+aseg is irrelevant - just the white and pial surfaces matter (and the spherical registration of course) cheers Bruce On Tue, 24 Mar 2009, Ryan Scotton wrote: Hi FreeSurfers, After a months of QC'ing FreeSurfer results, my team and I are now working toward end stage analysis of our cortical thickness data. All along, we have been aiming to make improvements in the wm.mgz volume so that we can assure that the white matter and gray matter surfaces are as accurate as possible. This was under the assumption that if the white matter and gray matter surfaces are accurate, then the voxel-wise representation of the white and gray matter in the aparc+aseg.mgz file would be accurate. However, in almost all of our cases, the aparc+aseg.mgz segmentation looks very bad. The bad aparc+aseg.mgz representation of what seem to be accurate white and gray matter segmentations in the wm.mgz file is leading us to believe that the cortical correspondences created after template mapping are wrong. Does anyone else have an explanation for such a discrepancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?
Hi guys, Does this mean that the measurements are probably solid, but the aparc+aseg.mgz volume inaccurately represents these measurements, or will I need to recompute the last two steps (aparc2aseg and wmparc) in order to attain accurate cortical thickness values? It doesn't like that way, since the thickness files are generated earlier in the recon stream. I ask this because we are trying to get the stats as fast as possible without having to rerun all of our cases (200+) over again. Ryan -- Forwarded message -- From: Bruce Fischl fis...@nmr.mgh.harvard.edu Date: Fri, Mar 27, 2009 at 2:47 PM Subject: Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume? To: Nick Schmansky ni...@nmr.mgh.harvard.edu Cc: Ryan Scotton ryan.scot...@gmail.com, Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Hi Ryan, I think a lot of the spottyness you are seeing is a bug in FS3 that was fixed. Try using the new FS to just regenerate the aparc+aseg and see if it looks better. Bruce On Fri, 27 Mar 2009, Nick Schmansky wrote: Ryan, Be sure to have a look at ribbon.mgz, as that is a volume file created using the white and pial surfaces (from mris_volmask), and would be the most accurate of the volume files in regards to gm segmentation. Nick On Fri, 2009-03-27 at 10:53 -0400, Ryan Scotton wrote: Hi Bruce, I've uploaded an example of a case with fairly accurate white and pial boundries when viewed on top of the wm.mgz volume, and GM areas that are not segmented and others which have a very fuzzy/noisy boundary within the aparc+aseg.mgz volume. Also, I'm not sure what email client you're using, but since my first email failed to come through, I ended up forwarding it and sending it to you again yesterday, which is the one you received. I noticed that in gmail, it will hide the quoted text, which contained my best description of the problems we're seeing and my FS version (3.0.4). You may have already read it, I'm not sure, but just in case, it's inline with this email. The file I uploaded is named 5008-003-02_scotton.tar.gz Thanks so much for your help, Ryan On Thu, Mar 26, 2009 at 5:36 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ryan, I still don't quite understand what I'm looking at. Maybe you can put a problem subject somewhere we can get to it? cheers, Bruce On Thu, 26 Mar 2009, Ryan Scotton wrote: For whatever reason, my email from this morning doesn't seem to have gone through. Hopefully it will work this time... Ryan -- Forwarded message -- From: Ryan Scotton ryan.scot...@gmail.com Date: Thu, Mar 26, 2009 at 10:25 AM Subject: Re: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume? To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Hello again Bruce, We used FreeSurfer version 3.0.4, so an older version. I've attached 9 screen shots...the first 6 are from the same subject, and the last three (the jpgs with _2 at the end of them) were included just to give a better idea of the problems we're seeing in the aparc +aseg.mgz volume, despite good surfaces in the wm.mgz volume (screenshots of the wm.mgz were not included for the 2nd volume...they are equally accurate as the first case I sent). You'll notice that there are many GM areas that are not segmented and others which have a very fuzzy/noisy boundary. Do you think that there is some kind of error occuring in the spherical registration step? If so, how can one QC this step? Or is it some other issue entirely? Thanks for your help, Ryan On Tue, Mar 24, 2009 at 5:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ryan, what version are you using? And when you say bad what exactly do you mean? Can you send some snapshots? If you're doing a thickness study the aparc+aseg is irrelevant - just the white and pial surfaces matter (and the spherical registration of course) cheers Bruce On Tue, 24 Mar 2009, Ryan Scotton wrote: Hi FreeSurfers, After a months of QC'ing
[Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?
Hi FreeSurfers, After a months of QC'ing FreeSurfer results, my team and I are now working toward end stage analysis of our cortical thickness data. All along, we have been aiming to make improvements in the wm.mgz volume so that we can assure that the white matter and gray matter surfaces are as accurate as possible. This was under the assumption that if the white matter and gray matter surfaces are accurate, then the voxel-wise representation of the white and gray matter in the aparc+aseg.mgz file would be accurate. However, in almost all of our cases, the aparc+aseg.mgz segmentation looks very bad. The bad aparc+aseg.mgz representation of what seem to be accurate white and gray matter segmentations in the wm.mgz file is leading us to believe that the cortical correspondences created after template mapping are wrong. Does anyone else have an explanation for such a discrepancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Version Discrepancies in Cortical Thickness Analysis?
Hi Bruce, My team has recently begun planning for data analysis after completing the overwhelming majority of our FreeSurfer runs and manual edits. However, it came to my attention that we do not currently have Qdec installed on our system...I realized that this is because we were using a very outdated version of FreeSurfer (3.0.4) that did not include Qdec. We have since downloaded the newest version so that we can begin data analysis, but this raises a bigger question: is it necessary for us to rerun FreeSurfer on all of our subjects (250+) if we are ONLY concerned with the white matter/grey matter surfaces and cortical thickness measurements? If not, spectacular. If so, is there only a small portion of the recon-all stream that we could run so that we could take care of this problem as fast as possible? Thanks! Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Viewing atlas?
Hi Freesurfers, Some associates of mine are working on a pipeline that generates cortical parcellations and we are looking to compare its measurements to some measurements generated by the freesurfer pipeline. However, our pipeline parcellates broader regions which include several labels generated by the FS cortical parcellation process within each of our labels. What we need is to get a general idea of where every label generated by FS fits within the context of our broader labeling scheme. SO, this may be an obvious question, but how might i be able to view an atlas image volume with the FS parcellation/labeling scheme applied to it in order to get a general idea of how the separate labeling schemes match up? Thanks! Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness issues
Hi all, I am fairly new to FreeSurfer and I've just finished initial runs on about 140 MRI images. Now, my job is to go through and do a little QC that helps ensure that the cortical thickness values are as accurate as possible. Now, I have a few questions: 1. Am I right in assuming that cortical thickness values are calculated as a function of the distance between the white and pial surfaces? 2. How exactly are the white and pial surfaces calculated? Do they utilize the wm segmentation? 3. Since I thought this was the case, I have tried cleaning up a couple images by using control points (using case 4 in the tutorial as a guide), hoping that the white and pial surfaces would be redrawn in a more accurate way. However, the problem remains. The surfaces are not including parts that are obviously white matter and gray matter. So basically, I'm thinking I'm missing something on the best way to fix white and pial surfaces when they're not accurate enough. Could anyone offer me some advice/a link to a site which explains the best way to handle such problems? Thanks, and sorry for the long post. Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] total brain volume correction
Hello, I was curious if anyone had specific recommendations for correcting ROIs for total brain volume/ICV. From what I can tell, some groups correct each ROI by computing a ratio of ROI/total_brain_volume. Other groups, however, enter total brain volume as a covariate in their statistical models. Both methods seem reasonable, but it seems entering total brain size as a covariate may be more robust, controlling for potential interactions with other IVs (e.g. age, gender). Are there other strategies I am missing? Any advice is much appreciated! Thanks! -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wmparc/white matter problems?
Hi Doug,
The white matter in aseg seems to follow the same pattern as the white
matter in wmparc...it goes into the ribbon (through the white matter
surface into gray matter).
-Ryan
On Dec 7 2007, Doug Greve wrote:
Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they
look in that area?
Ryan Muetzel wrote:
Hi Doug,
The images are attached. Thanks again for your help!
-Ryan
On Dec 6 2007, Doug Greve wrote:
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurfer version 4.0.1 and seem to be having
problems with the white matter/gray matter parcellation borders.
When viewing the pial and the main white surfaces in tkmedit,
everything looks good against the t1 brain. However, when the wmparc
is loaded on, we are seeing that the wmparc ROIs sometimes do not
follow the white surfacethe ROIs are going into the gray matter
regions.
Are the white matter surfaces converted to volumes and then
convolved with the aseg/aparcs/etc or are they only used for the
cortical thickness computations? It almost seems as if the intensity
based wm seg is used and not the wm surface based
(?h.dwhite.ribbon.mgz)?
Any help is much appreciated!
-Ryan
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[Freesurfer] Tutorial
In FreeSurferTutorial.pdf, starting on page 27 for examples on correcting holes and handles, why do the images in the original bert file appear as right hemisphere on left while the images in the tutorial appear as right hemisphere on right side? Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
