Freesurfer

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Re: [Freesurfer] FsFastPreProc Registration of files from each session to their session's structural image
by Ben Smith 20 Feb '18

20 Feb '18

Thanks - I very much appreciate your thorough explanation! We don't expect changes in the actual structure of the brain, but I am concerned about alignment of the structure in 3D space within the scanner. You're probably aware that when using software like FSL, it is typically advisable to align a functional image to a structural image taken in the same session. To my knowledge, this is because the software needs the high-resolution information in the structural image at the same position to correctly identify the position of the functional image in the same space. Could you confirm Freesurfer should be able to identify and align functional image even with a T1 from a different session where, for example, the subject's position in the scanner differs by several centimeters from one session to the next? On Tue, Feb 20, 2018 at 2:09 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > If you are combining the T1 images together in recon-all, then it is not > possible to separate them in FSFAST. If you do not expect structural > changes, then you can just register both fMRI sessions to the single > anatomical. If you are expecting changes, then analyze the T1 images > separately (in the longitudinal stream). This creates two subject names; > use the appropriate one in each fmri session. > > > On 02/16/2018 02:30 AM, Ben Smith wrote: > > (Thanks for your feedback to my previous inquiry - I've resolved this > > problem) > > > > I'm running FsFastPreProc on a dataset with a number of > > subjects, where each subject has two sessions. > > > > There's a separate structural image taken in each session. I want to > > make sure each subject's functional data is registered to the correct > > structural image. When running fsfast, setting up the file structure I > > can see clearly how FsFast uses the subjectname file to identify the > > right subject. It also seems easy enough to register multiple T1 > > images - just include multiple inputs for each subject to the > > *recon-all* command. > > > > But how do I map the session to the appropriate T1 image in the > > structural data? > > > > Also, if I were registering feat directories to structural using > > reg-feat2anat - how would I specify the session in that case? > > > > Does this even matter? Perhaps FSFastPreProc is built to process > > images without having a T1 from the same session as each image. > > > > If there's not an easy way to do this, would a suitable workaround be > > to create a separate anatomical subject folder for every subject*session? > > > > Thanks very much for your help! > > > > Best regards > > > > Ben > > > > > > _______________________ > > Ben Smith, MSc. > > Ph.D. Candidate > > University of Southern California > > https://bjsmith.github.io/ > > w | +1 213-740 7851 > > m | +1 323-385 9349 > > skype | ben.smith.nz <http://ben.smith.nz/> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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(a)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. >

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Subjectwise extraction from ROIs
by Sahil Bajaj 20 Feb '18

20 Feb '18

Hello experts, I identified two clusters (X for thickness and Y for volume) showing significant association between cortical measures (thickness and volume) and motor-performance. I followed steps from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and got several output files same as mentioned at the bottom of this page i.e. cache*.* I am interested in getting subject-wise thickness and volume values from these two clusters X and Y. >From previous posts, I found that these subjectwise cluster values (e.g. thickness and volume) are saved in *.ocn.dat file. If that's correct, I have following questions: (1). When I look at *.ocn.dat file, subjectwise thickness values range between 2-3 and volume values are in the range between 0-2. I am not sure if that makes sense and what are the units of thickness and volume here? (2). Since *.ocn.dat file for X gives subjectwise thickness value for cluster X and *.ocn.dat file for Y gives subjectwise volume values for cluster Y, so how can I get volume values for cluster X and thickness values for cluster Y? >From pervious FS discussion, I found that it can be done using *.ocn.annot files e.g. to extract volume values from X, *.ocn.annot for X can be used in mris_anatomical_stats file. To make sure and confirm that this is the correct approach, I calculated thickness values for X using this approach, expecting that these should match with *.ocn.dat for X but it's not matching. I also converted *.annot to *.label in native space following steps from https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html but still values are not matching with *.ocn.dat. I would really appreciate any help. Thanks, Sahil

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Using masks from aseg.mgz with mri_glmfit
by amirhossein manzouri 20 Feb '18

20 Feb '18

Hi , I did longitudinal analysis and now I made masks for Hippocampus and amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use the masks with mri_glmfit for volume_rate_stack but I get "dimensions mismatch 1 between y and mask" error . I wonder: 1) How can I run analysis in subcortical volumes? 2) Is it possible to run mri_glmfit on the whole brain not lh and rh separately ? Best regards, Amirhossein Manzouri

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FsFastPreProc Registration of files from each session to their session's structural image
by Ben Smith 20 Feb '18

20 Feb '18

(Thanks for your feedback to my previous inquiry - I've resolved this problem) I'm running FsFastPreProc on a dataset with a number of subjects, where each subject has two sessions. There's a separate structural image taken in each session. I want to make sure each subject's functional data is registered to the correct structural image. When running fsfast, setting up the file structure I can see clearly how FsFast uses the subjectname file to identify the right subject. It also seems easy enough to register multiple T1 images - just include multiple inputs for each subject to the *recon-all* command. But how do I map the session to the appropriate T1 image in the structural data? Also, if I were registering feat directories to structural using reg-feat2anat - how would I specify the session in that case? Does this even matter? Perhaps FSFastPreProc is built to process images without having a T1 from the same session as each image. If there's not an easy way to do this, would a suitable workaround be to create a separate anatomical subject folder for every subject*session? Thanks very much for your help! Best regards Ben _______________________ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.io/ w | +1 213-740 7851 m | +1 323-385 9349 skype | ben.smith.nz

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mri_robust_template output data size
by Chang, Yulin 20 Feb '18

20 Feb '18

Hello, Synopsis I have 5 longitudinally acquired high-res volumes at 0.8 mm isotropic resolution. The matrix size is 320x320x240 (240 is long left-right), covering an FOV of 256x256x192 mm3. I've used mri_robust_template to create a template out of these 5 volumes, preferably at the same matrix size and FOV. However, sometimes the matrix size of the created template is 321x321x321, resulting in the FOV of 256.8x256.8x192.8 mm3. This non-standard FOV would lead to error in the subsequent FreeSurfer segmentation analysis. Details The command I used was: $ mri_robust_template \ -- mov sub1_rep01.nii sub1_rep02.nii sub1_rep03.nii sub1_rep04.nii sub1_rep05.nii \ -- template sub1.nii \ -- lta sub1_rep01.lta sub1_rep02.lta sub1_rep03.lta sub1_rep04.lta sub1_rep05.lta \ -- mapmov rep01_to_mean.nii rep02_to_mean.nii rep03_to_mean.nii rep04_to_mean.nii rep05_to_mean.nii \ -- average 0 \ -- iscale \ -- satit The size of the output is NOT consistent: Sometimes the matrix becomes 320x320x320 (with the left-right FOV extended), but at other times it becomes 321x321x321. In the latter case, the FreeSurfer recon with -hires flag $ recon-all -i sub1.nii -subject recon_sub1 -all -hires -expert hires.expert-options would fail with the error message (from recon-all.log) ************************************** ERROR! FOV =256.799 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. ****************************************** (I am reluctant to explore the flag -cw256 for workflow reasons.) So why the output of mri_robust_template not consistent? Is there anything intrinsic in the data that would affect the output data size? 1) FreeSurfer version: freesurfer-Linux-centos_x86_64-stable-pub-v6.0.0-2bed96c 2) Platform: CentOS Linux release 7.4.1708 (Core) 3) uname -a: Linux host 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

1 0

Goodness of fit
by Sarah Cole 20 Feb '18

20 Feb '18

Hi Doug, I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there is any way to check the variance explained and fits on the model? Thank you, -S

2 2

Error in running make_average_subject
by M Janani 20 Feb '18

20 Feb '18

Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial Loading lh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial Loading rh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from Could you please help us in resolving the issue. Have also attached the recon-all log for reference. Thanks & Regards, Janani ::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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Segmenting the Corpus Callosum
by Benjamin Yeske 20 Feb '18

20 Feb '18

Hello Freesurfer Experts, I was looking through your website to see if I could find any info/papers that explained what landmarks you use for segmenting the corpus callosum, but I couldn't find anything on the topic. Could you please point me to a paper or resource that explains how freesurfer captures the corpus callosum and what landmarks it use to segment it out? We'd like to be able to hand check this region for accuracy in our TBI patients brain scans. Thank you, Ben

3 3

Requesting to unsubscription
by neha hooda 20 Feb '18

20 Feb '18

Dear Admin , Can you please remove me from the mailing list of freesurfer. With warm regards Neha

1 0

mris_flatten error: bad vertex
by Ji Won Bang 20 Feb '18

20 Feb '18

Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat It returns the error: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d with 30434 vertices (20.5% of total) MRISreadPatch: bad vertex # (148517) found in patch file No such file or directory When making the patch lh.oc.patch.3d, I followed the processes below: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As lh.oc.patch.3d So I think I made the patch correctly. ! weird thing that I suspect is that when I click save patch as, the default location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to $SUBJECTS_DIR/$SUBJECT/surf Could you please help me? Thanks a lot! Best, Ji Won

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