[Freesurfer] Parcellated regions as masks?
Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka___ 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] 2D representation of the cortex to get cortical thickness measure
Hi, Is it possible to get over some 2D representation of the cortex (whether it's on a plane, on the surface of a sphere, it doesn't matter (although the plane would probably be easiest to work with)) to get cortical thickness measures at every location? Thanks, --Mohammad This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original. ___ 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] Correspondence between label vertex number and time course
Dear experts I have created a larger number of labels on the FS_average surface and performed an FS_FAST analysis. The main goal is to obtain a functional connectome that contains all the possible correlations between 50 Rois in 100 subjects. The FS_fast analysis resulted in a fmcpr.sm5.subject.lh.nii.gz file. I assume that this file has been mapped to the FS_average surface using spherical alignment. Therefore the vertex numbers reported in the FS_average label may directly correspond with the column position of the time course in the two dimensional lh.nii.gz for any given subject. Is this correct? Or do I need to transform the lh.nii.gz with a spherical coreg file? Thanks in advance Cheers Jan ___ 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] Parcellated regions as masks?
establish a registration between the functional and anatomical with bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the function space. On 01/21/2015 01:52 PM, sabin khadka wrote: Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka ___ 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.
Re: [Freesurfer] mri_cnr and bash
My desirable output would be then a .txt file that consists of merely two columns. The first column is the subject's ID and the second is the CNR value only, for example: bruce 1.602 bert 1.555 john_doe 1.666 Thanks in advance. Cheers, Jacek Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a): Hi Jacek if you give us an example of what the desired output would be for you it would just be a couple of minutes to put it in the code. Or maybe someone can post some sed code (or some easy alternative) to parse the CNR out of the output. Bruce On Wed, 21 Jan 2015, Jacek Manko wrote: Oh, I thought it was already defined. I am referring actually to this thread... https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html ...and, allowing myself to specify my problem, when I type the command 'mri_cnr' what I become in my terminal is something more or less like that: mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gray/white CNR = 2.241, gray/csf CNR = 1.026 lh CNR = 1.633 white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gray/white CNR = 2.205, gray/csf CNR = 0.937 rh CNR = 1.571 total CNR = 1.602 My question is, if there is a way to export the CNR value, that is 1.602, to a seperate file alongside with the subject's ID. I suppose there are no such bulit-in commands in FreeSurfer, is that right? Thanks. Cheers, Jacek Manko Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a): how do you want to define CNR? On 01/21/2015 06:21 AM, Jacek Manko wrote: Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with a recon edit
Hi everyone I don't know if someone had the chance to look at the data we uploaded for advice to edit the recons (see below). Thank you so much Celine On Fri, 2015-01-16 at 11:43 -0500, Celine Louapre wrote: Thanks Bruce The aseg is correct, no ventricule labeled there (I was used to that) that I could see. I couldn't find the topological defect indeed, and what is strange if that the wrong surface on the right hemisphere were correct after autorecon2 but incorrect after autorecon3. The problem on the left hemisphere was already present after autorecon2. I have uploaded the recon directory there: https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/32464/1/2115a25100be43906c26359fbbd1ed08 Thank you again :-) Celine On Fri, 2015-01-16 at 11:03 -0500, Bruce Fischl wrote: Hi Celine hard to tell from the slices. Are there voxels labeled ventricle there? If so, you need to correct the aseg. If not, it's probably a topological defect that is fixed incorrectly. If you upload the subject we'll take a look Bruce On Fri, 16 Jan 2015, Celine Louapre wrote: Sorry forgot the attachement :-) Hi Freesurfer team We have been struggling with editing recon for one patient, see the 2 slices attached. The problem is that the surface don't go all the way up to the bottom of the sulci. I had this some times before but usually managed to fix it with editing the wm and the aseg, but this time I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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 ___ 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] 2D representation of the cortex to get cortical thickness measure
Hi Mohammad, the thickness can be displayed as a map on any surface we create. We do create ?h.sphere files by default, so you can use those if you want. If you'd rather a planar representation you need to make cuts in the inflated surface and use mris_flatten. cheers Bruce On Wed, 21 Jan 2015, Zia, Mohammad wrote: Hi, Is it possible to get over some 2D representation of the cortex (whether it's on a plane, on the surface of a sphere, it doesn't matter (although the plane would probably be easiest to work with)) to get cortical thickness measures at every location? Thanks, --Mohammad This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original. ___ 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_cnr and bash
Oh, I thought it was already defined. I am referring actually to this thread... https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html ...and, allowing myself to specify my problem, when I type the command 'mri_cnr' what I become in my terminal is something more or less like that: mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gray/white CNR = 2.241, gray/csf CNR = 1.026 lh CNR = 1.633 white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gray/white CNR = 2.205, gray/csf CNR = 0.937 rh CNR = 1.571 total CNR = 1.602 My question is, if there is a way to export the CNR value, that is 1.602, to a seperate file alongside with the subject's ID. I suppose there are no such bulit-in commands in FreeSurfer, is that right? Thanks. Cheers, Jacek Manko Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a): how do you want to define CNR? On 01/21/2015 06:21 AM, Jacek Manko wrote: Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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
Re: [Freesurfer] mri_cnr and bash
Hi Jacek if you give us an example of what the desired output would be for you it would just be a couple of minutes to put it in the code. Or maybe someone can post some sed code (or some easy alternative) to parse the CNR out of the output. Bruce On Wed, 21 Jan 2015, Jacek Manko wrote: Oh, I thought it was already defined. I am referring actually to this thread... https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html ...and, allowing myself to specify my problem, when I type the command 'mri_cnr' what I become in my terminal is something more or less like that: mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gray/white CNR = 2.241, gray/csf CNR = 1.026 lh CNR = 1.633 white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gray/white CNR = 2.205, gray/csf CNR = 0.937 rh CNR = 1.571 total CNR = 1.602 My question is, if there is a way to export the CNR value, that is 1.602, to a seperate file alongside with the subject's ID. I suppose there are no such bulit-in commands in FreeSurfer, is that right? Thanks. Cheers, Jacek Manko Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a): how do you want to define CNR? On 01/21/2015 06:21 AM, Jacek Manko wrote: Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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 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] converting .nii to .mgz
Also, i didn't attach the error I got- please see attached. Thanks! m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Tuesday, January 20, 2015 4:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] converting .nii to .mgz It was initially in the wrong folder, but now it in the mri folder. ls -l /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz -rw-rw-r-- 1 miaborz acqcash 15954217 Jan 20 16:16 /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz Still unable to load with tkmedit though. Thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, January 20, 2015 3:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting .nii to .mgz does /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz exist? On 01/20/2015 03:40 PM, Borzello, Mia wrote: Okay, cool, I just tried with the full path to the .nii file and it worked. However, when I tried to load the ct.anat.mgz using tkmedit i get an error in loading the volume. FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects 1) MG17 2) tkmedit MG17_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz 3) this is the error: mghRead(/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz, -1): could not open file Converting main surface: 100% done. Converting main surface: 100% done. Converting original surface: 100% done. Converting pial surface: 100% done. Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl and the grey box pops up saying it couldn't load the volume. (not sure if I should start a new thread for this or not). Thanks again for all your help, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, January 20, 2015 2:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting .nii to .mgz I was able to convert your file without problem. When you run mri_convert, you have to give a path to a file that exists. Below, the error says that it cannot find /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii Does this file exist? It is different than the one you have below, ie /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii On 01/20/2015 11:26 AM, Borzello, Mia wrote: Hi guys, full command line: mri_convert ct.anat.nii ct.anat.mgz command line: ls -l /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii -rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii I had to send the ct.anat.nii file separately because it was too large of a file for this email. Thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, January 20, 2015 7:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] converting .nii to .mgz Hi Mia can you please send us the full command line? And also do an ls -l of that file and include it? thanks Bruce On Tue, 20 Jan 2015, Borzello, Mia wrote: Hi Bruce, Thanks for getting back to me so quickly! I just tried that and got the following error: reading from ct.anat.nii... niiRead(): error opening file /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii I'm wondering if the nifti file is possibly corrupted. Is there a way to check this? Thanks so much, Mia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 19, 2015 10:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] converting .nii to .mgz Hi Mia If all you want to do is convert try mri_convert
Re: [Freesurfer] Correspondence between label vertex number and time course
You are correct. Note that if you want to compute an average inside of a label, that you may want to use fMRI data that is unsmoothed (even on the surface) as this will cause false correlations between labels. doug On 01/21/2015 01:16 PM, Jan Willem Koten wrote: Dear experts I have created a larger number of labels on the FS_average surface and performed an FS_FAST analysis. The main goal is to obtain a functional connectome that contains all the possible correlations between 50 Rois in 100 subjects. The FS_fast analysis resulted in a 'fmcpr.sm5.subject.lh.nii.gz' file. I assume that this file has been mapped to the FS_average surface using spherical alignment. Therefore the vertex numbers reported in the FS_average label may directly correspond with the column position of the time course in the two dimensional lh.nii.gz for any given subject*.* *Is this correct?* *Or do I need to transform the lh.nii.gz with a spherical coreg file? * Thanks in advance Cheers Jan ___ 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] QDEC group comparisons
Hi Everyone, I have been using both tksurfer and QDEC to view group comparisons of cortical thickness maps. One advantage of using tksurfer has been the ability to view various measures such as mean, tval, and stderr. Is there any way of viewing maps other than just the mean thickness/volume/etc. on QDEC? Thanks for your help, Kelly ___ 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] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model
You will need a 4 group FSGD. The interaction would be contrast 7 on the 4G web page doug On 01/21/2015 09:38 AM, lindsay hanford wrote: Hello Doug, Thank you for your reply. I misused the word contrast, when I should have said design matrix. It looks at though I should be able to look at an interaction effect between two variables but ignore another. In the case of the example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V you could be able to look at the interaction between Group and Age while ignoring (or controlling) for the effects of weight. But maybe this is not possible to do with a categorical variable? I have also considered using a four group design as shown in https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, where you concatenate two categorical variables however, I dont think you can look at interaction effects between those variables anymore. So I'm still wondering if it is possible to look at the interaction between two categorical variables using fsgd? GroupDescriptorFile 1 #Title SZ vs HC Class HC Class SZ Variables Score Sex Age Input 130 HC high m 50 Input 277 HC low f 53 Input 190 HC low m 25 Input 201 SZ high f 29 Input 250 SZ high f 52 ... Group difference.mtx 1 -1 0 0 0 0 0 0 Group by Score interaction .mtx 0 0 1 -1 0 0 0 0 But this doesn't and should work. How should I proceed? Thanks again, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study| *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784***|*lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com ___ 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.
Re: [Freesurfer] mri_cnr and bash
how do you want to define CNR? On 01/21/2015 06:21 AM, Jacek Manko wrote: Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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.
Re: [Freesurfer] mri_cnr and bash
actually if you run mri_cnr with -l out.log it will write a line to out.log of the form: gray_white_cnr gray_csf_cnr white_mean gray_mean csf_mean sqrt(white_var) sqrt(gray_var) sqrt(csf_var)) so you would create one file for each subject. You could then run a for loop over your subjects to cat them into a single file cheers Bruce On Wed, 21 Jan 2015, Jacek Manko wrote: My desirable output would be then a .txt file that consists of merely two columns. The first column is the subject's ID and the second is the CNR value only, for example: bruce 1.602 bert 1.555 john_doe 1.666 Thanks in advance. Cheers, Jacek Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a): Hi Jacek if you give us an example of what the desired output would be for you it would just be a couple of minutes to put it in the code. Or maybe someone can post some sed code (or some easy alternative) to parse the CNR out of the output. Bruce On Wed, 21 Jan 2015, Jacek Manko wrote: Oh, I thought it was already defined. I am referring actually to this thread... https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html ...and, allowing myself to specify my problem, when I type the command 'mri_cnr' what I become in my terminal is something more or less like that: mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz processing MRI volume /homes/4/fischl/local_subjects/bruce/mri/norm.mgz... white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2 gray/white CNR = 2.241, gray/csf CNR = 1.026 lh CNR = 1.633 white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4 gray/white CNR = 2.205, gray/csf CNR = 0.937 rh CNR = 1.571 total CNR = 1.602 My question is, if there is a way to export the CNR value, that is 1.602, to a seperate file alongside with the subject's ID. I suppose there are no such bulit-in commands in FreeSurfer, is that right? Thanks. Cheers, Jacek Manko Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a): how do you want to define CNR? On 01/21/2015 06:21 AM, Jacek Manko wrote: Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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 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.
Re: [Freesurfer] mri_cnr and bash
would something like this work?
set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf
$SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
echo $subject $cnr yourfile
On 01/21/2015 02:46 PM, Jacek Manko wrote:
My desirable output would be then a .txt file that consists of merely two
columns. The first column is the subject's ID and the second is the CNR value
only, for example:
bruce 1.602
bert 1.555
john_doe 1.666
Thanks in advance.
Cheers,
Jacek
Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a):
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or maybe someone
can post some sed code (or some easy alternative) to parse the CNR out of
the output.
Bruce
On Wed,
21 Jan 2015, Jacek Manko wrote:
Oh, I thought it was already defined. I am referring actually to this
thread...
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html
...and, allowing myself to specify my problem, when I type the command
'mri_cnr' what I become in my terminal is something more or less like
that:
mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/norm.mgz
processing MRI volume
/homes/4/fischl/local_subjects/bruce/mri/norm.mgz...
white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2
gray/white CNR = 2.241, gray/csf CNR = 1.026
lh CNR = 1.633
white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4
gray/white CNR = 2.205, gray/csf CNR = 0.937
rh CNR = 1.571
total CNR = 1.602
My question is, if there is a way to export the CNR value, that is
1.602, to a seperate file alongside with the subject's ID. I suppose
there are no such bulit-in commands in FreeSurfer, is that right?
Thanks.
Cheers,
Jacek Manko
Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a):
how do you want to define CNR?
On 01/21/2015 06:21 AM, Jacek Manko wrote:
Dear All,
I have been wondering if there is a way (already implemented in the
FreeSurfer) to export CNR measurement outputs to seperate file, like a
table or someting. If not, it will possible only via some pretty
advanced bash scripting, am I right? If so, has anyone some experience
with that matter?
Thanks.
Cheers,
Jacek Manko
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Fax: 617-726-7422
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Phone Number: 617-724-2358
Fax: 617-726-7422
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Re: [Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model
Thank you for you help! Yes the contrast 7 in the group 4 example makes complete sense. However, I am still left with not being able to control for the effects of another categorical variable. For example I can look at the interaction of Group X Score, but for this I need to remove the categorical variable sex (M/F): GroupDescriptorFile 1 #Title SZ vs HC Class HChigh Class HClow Class SZhigh Class SZlow Variables Score Age Input 130 HChigh 50 Input 277 HClow 53 Input 190 HClow 25 Input 201 SZhigh 29 Input 250 SZhigh 52 ... Group difference.mtx 0.5 -0.5 -0.5 0.5 0 0 0 0 However, I understand how important it is to control for the effects of sex. Am I better to try 8 groups? GroupDescriptorFile 1 #Title SZ vs HC Class HCmhigh Class HCfhigh Class HCmlow Class HCflow Class SZmhigh Class SZfhigh Class SZmlow Class SZflow Variables Age Input 130 HCmhigh 50 Input 277 HCflow 53 Input 190 HCmlow 25 Input 201 SZfhigh 29 Input 250 SZfhigh 52 ... Group difference.mtx 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 Heres where I am confused: Group by Score interaction.mtx could either be: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 or perhaps? 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 Once again, thank you in advance!! Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study | *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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] Parcellated regions as masks?
If you run it with --help you'll see several examples. On 01/21/2015 03:21 PM, sabin khadka wrote: Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use mri_label2vol to map the aparc+aseg.mgz into the function space ( I could not find the correct syntax that should be used)? Also, what should i do if I want individual masks for each ROI? Cheers, Sabin Khadka *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, January 21, 2015 1:59 PM *Subject:* Re: [Freesurfer] Parcellated regions as masks? establish a registration between the functional and anatomical with bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the function space. On 01/21/2015 01:52 PM, sabin khadka wrote: Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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 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 -- 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
[Freesurfer] Custom color lookup table
Hi all, I recently installed freesurfer on my mac, and I'm having a small problem with freeview. If I load a segmentation file, and then try to associate it with a custom color lookup table, freeview stops responding. Even if I was to use an exact copy of /Applications/freesurfer/FreeSurferColorLUT.txt, the problem still persists: cp -i /Applications/freesurfer/FreeSurferColorLUT.txt \ ~/Documents/CustomColor.txt I will try to re-install the program, but I first wanted to check if anyone has ever encountered issues with custom color tables. See info below: MacBook Air (13) OS X Yosemite (Version 10.10) Processor: 1,4 GHz Intel Core i5; x86_64) Memory: 4GB 1600 MHz DDR3 I first downloaded XQuartz 2.7.6 and then downloaded/installed latest versions of freesurfer and freeview: http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview I'd really appreciate your feedback. Thank you very much!___ 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] Parcellated regions as masks?
Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use mri_label2vol to map the aparc+aseg.mgz into the function space ( I could not find the correct syntax that should be used)? Also, what should i do if I want individual masks for each ROI? Cheers, Sabin Khadka From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, January 21, 2015 1:59 PM Subject: Re: [Freesurfer] Parcellated regions as masks? establish a registration between the functional and anatomical with bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the function space. On 01/21/2015 01:52 PM, sabin khadka wrote: Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka ___ 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 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] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model
The Group by Score interaction.mtx is indeed 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 On 01/21/2015 03:26 PM, lindsay hanford wrote: Thank you for you help! Yes the contrast 7 in the group 4 example makes complete sense. However, I am still left with not being able to control for the effects of another categorical variable. For example I can look at the interaction of Group X Score, but for this I need to remove the categorical variable sex (M/F): GroupDescriptorFile 1 #Title SZ vs HC Class HChigh Class HClow Class SZhigh Class SZlow Variables Score Age Input 130 HChigh 50 Input 277 HClow 53 Input 190 HClow 25 Input 201 SZhigh 29 Input 250 SZhigh 52 ... Group difference.mtx 0.5 -0.5 -0.5 0.5 0 0 0 0 However, I understand how important it is to control for the effects of sex. Am I better to try 8 groups? GroupDescriptorFile 1 #Title SZ vs HC Class HCmhigh Class HCfhigh Class HCmlow Class HCflow Class SZmhigh Class SZfhigh Class SZmlow Class SZflow Variables Age Input 130 HCmhigh 50 Input 277 HCflow 53 Input 190 HCmlow 25 Input 201 SZfhigh 29 Input 250 SZfhigh 52 ... Group difference.mtx 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 Heres where I am confused: Group by Score interaction.mtx could either be: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 or perhaps? 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 Once again, thank you in advance!! Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study| *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784***|*lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com ___ 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.
Re: [Freesurfer] QDEC group comparisons
No, sorry. doug On 01/21/2015 01:02 PM, Leyden, Kelly wrote: Hi Everyone, I have been using both tksurfer and QDEC to view group comparisons of cortical thickness maps. One advantage of using tksurfer has been the ability to view various measures such as mean, tval, and stderr. Is there any way of viewing maps other than just the mean thickness/volume/etc. on QDEC? Thanks for your help, Kelly ___ 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.
Re: [Freesurfer] Custom color lookup table
I can confirm this bug on Mac (It does not happen on Linux). I'll look into it. Best, Ruopeng On 01/21/2015 03:11 PM, Mateus Aranha wrote: Hi all, I recently installed freesurfer on my mac, and I'm having a small problem with freeview. If I load a segmentation file, and then try to associate it with a custom color lookup table, freeview stops responding. Even if I was to use an exact copy of /Applications/freesurfer/FreeSurferColorLUT.txt, the problem still persists: cp -i /Applications/freesurfer/FreeSurferColorLUT.txt \ ~/Documents/CustomColor.txt I will try to re-install the program, but I first wanted to check if anyone has ever encountered issues with custom color tables. See info below: MacBook Air (13) OS X Yosemite (Version 10.10) Processor: 1,4 GHz Intel Core i5; x86_64) Memory: 4GB 1600 MHz DDR3 I first downloaded XQuartz 2.7.6 and then downloaded/installed latest versions of freesurfer and freeview: http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview I'd really appreciate your feedback. Thank you very much! ___ 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.
Re: [Freesurfer] Correspondence between label vertex number and time course
thank you smoothing=shit; cheers jan Gesendet:Mittwoch, 21. Januar 2015 um 20:01 Uhr Von:Douglas N Greve gr...@nmr.mgh.harvard.edu An:freesurfer@nmr.mgh.harvard.edu Betreff:Re: [Freesurfer] Correspondence between label vertex number and time course You are correct. Note that if you want to compute an average inside of a label, that you may want to use fMRI data that is unsmoothed (even on the surface) as this will cause false correlations between labels. doug On 01/21/2015 01:16 PM, Jan Willem Koten wrote: Dear experts I have created a larger number of labels on the FS_average surface and performed an FS_FAST analysis. The main goal is to obtain a functional connectome that contains all the possible correlations between 50 Rois in 100 subjects. The FS_fast analysis resulted in a fmcpr.sm5.subject.lh.nii.gz file. I assume that this file has been mapped to the FS_average surface using spherical alignment. Therefore the vertex numbers reported in the FS_average label may directly correspond with the column position of the time course in the two dimensional lh.nii.gz for any given subject*.* *Is this correct?* *Or do I need to transform the lh.nii.gz with a spherical coreg file? * Thanks in advance Cheers Jan ___ 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 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_cnr and bash
Dear All, I have been wondering if there is a way (already implemented in the FreeSurfer) to export CNR measurement outputs to seperate file, like a table or someting. If not, it will possible only via some pretty advanced bash scripting, am I right? If so, has anyone some experience with that matter? Thanks. Cheers, Jacek Manko ___ 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] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model
Hello Doug, Thank you for your reply. I misused the word contrast, when I should have said design matrix. It looks at though I should be able to look at an interaction effect between two variables but ignore another. In the case of the example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V you could be able to look at the interaction between Group and Age while ignoring (or controlling) for the effects of weight. But maybe this is not possible to do with a categorical variable? I have also considered using a four group design as shown in https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, where you concatenate two categorical variables however, I dont think you can look at interaction effects between those variables anymore. So I'm still wondering if it is possible to look at the interaction between two categorical variables using fsgd? GroupDescriptorFile 1 #Title SZ vs HC Class HC Class SZ Variables Score Sex Age Input 130 HC high m 50 Input 277 HC low f 53 Input 190 HC low m 25 Input 201 SZ high f 29 Input 250 SZ high f 52 ... Group difference.mtx 1 -1 0 0 0 0 0 0 Group by Score interaction .mtx 0 0 1 -1 0 0 0 0 But this doesn't and should work. How should I proceed? Thanks again, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery Study | *Department of Psychology, Neuroscience Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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.
