Re: [Freesurfer] uploading a surface in freeview
Hi Lilla, I still have the problem to display my surface created by the Monte Carlo analysis. There are several files generated and I think that mc-z.abs.2.sig.cluster.mgh should be the correct one to show the overlay in freeview. Could you please tell me which complete command I have to type in after opening freesurfer? Thank you very much. Best regards, Carina Gesendet:Mittwoch, 16. Juli 2014 um 14:01 Uhr Von:Lilla Zollei lzol...@nmr.mgh.harvard.edu An:Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff:Re: [Freesurfer] uploading a surface in freeview Hi Carina, You can use the -f option (instead of -v used for volumes) when you are calling freeview from the commandline in order to display a surface and then append :overlay=overlay_filename after the filename to identify the overlay that you want to use. You will need to decide which hemi and which surface you want to use and type the full path to it and the same with the overlay. Lilla On Wed, 16 Jul 2014, car...@van-vlodrop.de wrote: Dear Freesurfer experts, I have already run a Monte Carlo Simulation and I would like to upload the results in freeview. The simulation created a file ending with .mgh and the tutorial identifies it to be the overlay. Do I have to upload a surface first and afterwards the overlay? How can I upload a surface and which is the right one?Yours sincerely, Carina ___ 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 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] Repost: problem with mri_label2label - large amount of holes
Hi Zeke, we are getting a license file error: ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/.license How should we proceed? Thanks, Caspar On Wednesday, August 5, 2015, zkauf...@nmr.mgh.harvard.edu wrote: Hello Caspar, I did a quick test and it appears the new dev version of mri_label2label is still compatible with the version of 5.1 that you have. Please use the following link to download it and also please make sure to back up the version you already have. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/mri_label2label -Zeke Hi Bruce, Doug, and Zeke, just checking back regarding the dev version for mri_label2label. Do you have a build that works on MAC OS 10.9.5 Mavericks? So far, we have been using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. Thank you, Caspar 2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu javascript:; : We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard- i686-stable-pub-v5.1.0 On Thursday, July 30, 2015, Bruce Fischl fis...@nmr.mgh.harvard.edu javascript:; wrote: Hi Caspar the dev version of label2label doesn't have this problem. If you let us know your hardware/software environment Zeke can get you a new binary that should fix this issue cheers Bruce On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote: Hi Bruce and Doug, thanks for looking into this and sorry for the delay. The command line we are using is: mri_label2label --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p 8.label --srcsubject y$1 --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp 2.label --trgsubject yx$1 --regmethod surface --hemi lh We have several anatomies from the same subject, acquired on different occasions. We defined labels based on results of an fMRI experiment, and tried to use mri_label2label to map them within subjects from one anatomy to another. As a control, we also wanted to map the Hinds V1 from one anatomy to another, but this is where we ran into these holes. We will make an example subject available for debugging later today. Thanks! Caspar 2015-07-24 12:33 GMT-04:00 Douglas Greve gr...@nmr.mgh.harvard.edu javascript:;: what is your command line? What do you mean by one anatomy to another? On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: -- Forwarded message -- From: Caspar M. Schwiedrzik cschwie...@rockefeller.edu javascript:; Date: Thursday, July 16, 2015 Subject: problem with mri_label2label - large amount of holes To: Freesurfer@nmr.mgh.harvard.edu javascript:; freesurfer@nmr.mgh.harvard.edu javascript:; Hi! We are doing some analyses in which we map custom labels from one anatomy to another, within subjects. As a control, we also tried to map anatomically defined V1s according to the method by Hinds within subject from one anatomy to another. However, as you can see in the attachment, there are very many holes in the labels after using mri_label2label. This does not happen with smaller labels. Why is this happening and is there a solution? Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; 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 javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; 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
Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s
Hi Andre it's up to you. The aparc and .aparc.DKTatlas40 are probably pretty similar, although we haven't looked at the .aparc.DKTatlas40 much. The aparc.a2009s contains more, smaller parcels, and so is probably less reliable but might correspond more closely to an anatomical hypothesis you have. cheers Bruce On Sun, 9 Aug 2015, Son, Andre wrote: Hello, What is the difference b/w the data generated in .aparc vs .aparc.DKTatlas40. vs. aparc.a2009s? Which data should I be using for studies on cortical thickness? Thank you, AS This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = ___ 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] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s
Andre, I haven't done any statistical comparison, but for my data (pediatric) I found the DKT labels to be somewhat more accurate. The biggest differences were in superior frontal and rostral middle frontal. Other differences I've seen are anterior cingulate, cuneus, and fusiform. See Figure 4 in Klein Tourville (2012). RE your command example: have you tried including the full path for the images? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Son, Andre [andre@med.nyu.edu] Sent: Sunday, August 09, 2015 11:41 AM To: Freesurfer support list Subject: Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s Thank you Bruce. You're alway so helpful, even on the weekend! I'm also trying to convert mgz to nii and have been following various instructions online but can't seem to figure it out. For ease, I made a separate folder on the desktop with just mgz files in separate subject folders and ran the following commands verbatim: mri_convert --in_type mgz --out_type nii --out_orientation RAS /mnt/ .../desktop/mgz/001/t1.mgz /mnt/ .../t1.nii.gz I've also tried: mri_convert /desktop/mgz/001/t1.mgz /desktop/mgz/001/t1.nii.gz However, neither have worked, saying mghRead(/desktop/mgz/001/t1.mgz, -1) could not open file Any suggestions? Thank you. AS ___ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, August 09, 2015 11:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s Hi Andre it's up to you. The aparc and .aparc.DKTatlas40 are probably pretty similar, although we haven't looked at the .aparc.DKTatlas40 much. The aparc.a2009s contains more, smaller parcels, and so is probably less reliable but might correspond more closely to an anatomical hypothesis you have. cheers Bruce On Sun, 9 Aug 2015, Son, Andre wrote: Hello, What is the difference b/w the data generated in .aparc vs .aparc.DKTatlas40. vs. aparc.a2009s? Which data should I be using for studies on cortical thickness? Thank you, AS This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurferd=BQIBAgc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4m=rBhba0zG3mgP4Aqn5G5Bd4ykWLjO6caA21CXBwNEKWks=blc-wqbJC5fq0aep5_wLVqBOh-t9SWDMg8M1YM28mfce= 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compliancelined=BQIBAgc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4m=rBhba0zG3mgP4Aqn5G5Bd4ykWLjO6caA21CXBwNEKWks=VOvzL8DECTSlKu8aoIbME6JJAkkoOiaBxgpm1zjabvoe= . 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
Re: [Freesurfer] options for 7T images...
Hi Gonzalo Jon and Kyoko (both ccd) have put together a 7T stream, and should be able to help you out cheers Bruce On Sat, 8 Aug 2015, Gonzalo Rojas Costa wrote: Hi: Must I use any recon-all option for 7T images ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] options for 7T images...
sorry, had an old address for Kyoko On Sun, 9 Aug 2015, Bruce Fischl wrote: Hi Gonzalo Jon and Kyoko (both ccd) have put together a 7T stream, and should be able to help you out cheers Bruce On Sat, 8 Aug 2015, Gonzalo Rojas Costa wrote: Hi: Must I use any recon-all option for 7T images ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] uploading a surface in freeview
Hi Carina it should be something like: freeview -f path to surface/lh.inflated:overlay=mc-z.abs.2.sig.cluster.mgh assuming mc-z.abs.2.sig.cluster.mgh is in your current directory cheers Bruce On Sun, 9 Aug 2015, car...@van-vlodrop.de wrote: Hi Lilla, I still have the problem to display my surface created by the Monte Carlo analysis. There are several files generated and I think that 'mc-z.abs.2.sig.cluster.mgh' should be the correct one to show the overlay in freeview. Could you please tell me which complete command I have to type in after opening freesurfer? Thank you very much. Best regards, Carina Gesendet: Mittwoch, 16. Juli 2014 um 14:01 Uhr Von: Lilla Zollei lzol...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] uploading a surface in freeview Hi Carina, You can use the -f option (instead of -v used for volumes) when you are calling freeview from the commandline in order to display a surface and then append :overlay=overlay_filename after the filename to identify the overlay that you want to use. You will need to decide which hemi and which surface you want to use and type the full path to it and the same with the overlay. Lilla On Wed, 16 Jul 2014, car...@van-vlodrop.de wrote: Dear Freesurfer experts, I have already run a Monte Carlo Simulation and I would like to upload the results in freeview. The simulation created a file ending with .mgh and the tutorial identifies it to be the overlay. Do I have to upload a surface first and afterwards the overlay? How can I upload a surface and which is the right one? Yours sincerely, Carina ___ 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 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] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s
Thank you Bruce. You're alway so helpful, even on the weekend! I'm also trying to convert mgz to nii and have been following various instructions online but can't seem to figure it out. For ease, I made a separate folder on the desktop with just mgz files in separate subject folders and ran the following commands verbatim: mri_convert --in_type mgz --out_type nii --out_orientation RAS /mnt/ .../desktop/mgz/001/t1.mgz /mnt/ .../t1.nii.gz I've also tried: mri_convert /desktop/mgz/001/t1.mgz /desktop/mgz/001/t1.nii.gz However, neither have worked, saying mghRead(/desktop/mgz/001/t1.mgz, -1) could not open file Any suggestions? Thank you. AS ___ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, August 09, 2015 11:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s Hi Andre it's up to you. The aparc and .aparc.DKTatlas40 are probably pretty similar, although we haven't looked at the .aparc.DKTatlas40 much. The aparc.a2009s contains more, smaller parcels, and so is probably less reliable but might correspond more closely to an anatomical hypothesis you have. cheers Bruce On Sun, 9 Aug 2015, Son, Andre wrote: Hello, What is the difference b/w the data generated in .aparc vs .aparc.DKTatlas40. vs. aparc.a2009s? Which data should I be using for studies on cortical thickness? Thank you, AS This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = ___ 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] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s
Hello, What is the difference b/w the data generated in .aparc vs .aparc.DKTatlas40. vs. aparc.a2009s? Which data should I be using for studies on cortical thickness? Thank you, AS This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = ___ 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] segmentation fault while running -hippocampal-subfields-T1 flag
Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ 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] selxavg3-sess, -svres
Hi Doug, In order to understand my data better, I did the following analysis. First, I did a full model analysis with all stimuli conditions included in the analysis using: mkanalysis-sess -fsd bold -paradigm xy_mky_category_eye_weights.par -event-related -refeventdur 1 -no-inorm -delay 0 -polyfit 3 -gammafit 0 8 -gammaexp 0.3 -nuisreg mcprextreg 3 -nuisreg eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2. -nconditions 940 -funcstem f.mc.perrun.so.nativespace -acfbins 3 -analysis perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run -native -force -tpexclude xy_eye_tpe -runlistfile xyrunlist. Then I run: selxavg3-sess -s beck -d . -analysis perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -no-preproc -no-con-ok -overwrite -svres second, I did a analysis without the stimuli conditions: mkanalysis-sess -fsd bold -paradigm xy_mky_category_eye_weights.par -notask -no-inorm -delay 0 -nuisreg mcprextreg 3 -nuisreg eye_movTR_xy 2 -nuisreg fsl_DAVRS 1 -TR 2. -funcstem f.mc.perrun.so.nativespace -acfbins 3 -analysis NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -per-run -native -force -tpexclude xy_eye_tpe -runlistfile xyrunlist. Then, I runselxavg3-sess -s beck -d . -analysis NOtask_perrun_eye_weights_eyeMovTRxy_tpe_fslmotoutlier -no-preproc -no-con-ok -overwrite -svres After that, I loaded the residuals (res-00x.nii under the res directories) generated from the full model analysis and those from the no task analysis into the matlab. I expected that the results should be different, but the residuals from the two analysis are almost identical (correlation is 0.98) for a voxel where the stimuli from different conditions should cause significant response difference. Then, I tried to generated the residual from the full model analysis by real signal - design matrix (loaded from X.mat) *beta values (loaded into matlab from beta.nii). This residual is different from the residual of the NO task analysis. My question is why the residual from the two different analysis generated by fsfast are same? Are my commands wrong? Or the model is wrong? Second, it is possible to generate raw residuals without some kind of normalization? Thanks very much for your help! Xiaomin ___ 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] mri_deface
Dear Bruce thanks for the idea Cheers Jürgen Am 07.08.15 17:00 schrieb Bruce Fischl unter freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu: Hi Jurgen why not just use the defaced T1 as a mask for the DTI? Bruce On Fri, 7 Aug 2015, Jürgen Hänggi wrote: Dear FS experts I have to anonymize T1-w. and DTI images. I run mri_deface for T1-w. images successfully, but I am wondering whether there is any easy way to also deface DTI images with mri_deface or whether someone has already defaced DTI images with another tool. Thanks in advance Best regards Jürgen Hänggi - -- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. - -- ___ 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
Re: [Freesurfer] visualizing paths stats by voxel
Hi Anastasia, yes, I am. But it looks similar in the distributed version :( Thanks, Janosch Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Are you by any chance using the dev version of freeview? a.y On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia and list, I'm trying to do analyses along the tract with the path_stats_byvoxel files. When I am visualizing the points using the waypoint functionality of Freeview, it looks a little strange, i.e., the points are not equally spaces on the tract, but clumped together at some parts and spread out on others, see: this looks different to your slides: Also, the most posterior points seem to be strangely located (in the other hemisphere). What could be the reason for this strange behavior? Thanks, Janosch 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
