Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30079 discussions

applying a transform to volumes + surfaces?
by Jamie Hanson 10 Apr '08

10 Apr '08

Hi Freesurfers- Apologies for my recent multitude of questions (and big thanks for Bruce and colleagues for all their fabulous troubleshooting!). But I was wondering about applying transforms to my freesurfer data. I know this was asked on the listserv re: transformation on other dataset, but I thought my question was a bit different. I ran recon-all on data in native space images, but want to have them in AC-PC space. I presume I can import them into Matlab and apply a transform. Does anyone experience doing this? Any issues? Can you apply transforms to the cortical surfaces? With the Cortical Parcellations (and labels)? Is that even possible? Thanks much, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

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optseq2: error while loading
by BumSeok Jeong 09 Apr '08

09 Apr '08

Dear Expert, I got an error after typing optseq2 on my 64 bit FC5 system. optseq2: error while loading shared libraries: libstdc++.so.5: wrong ELF class: ELFCLASS64 uname -m reported x86_64 Thank you, bumseok

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glmdir
by Jerry Yeou-Wei Chen 09 Apr '08

09 Apr '08

Hi, Just a very quick question about the glmdir flag for mri_glmfit when running the group analysis via command line: If I am interested in multiple contrasts, can glmdir be the same for subsequent iterations of mri_glmfit with different contrast vectors? (I understand that each contrast comes up as a corresponding subdirectory... but are there any issues with overwriting any files in the glmdir?) Thanks, - Jerry

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Interactions for continuous variables
by Jerry Yeou-Wei Chen 09 Apr '08

09 Apr '08

Hello, I would like to know how to examine an interaction between continuous variables. In SPM, my understanding is that a new interaction regressor, comprised of the product of the two continuous variables of interest, can be coded and entered into the model. Would this be appropriate for CTA group analysis in FreeSurfer? Is there any difference if I use the old command line method or the QDEC GUI? Thanks, - Jerry

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Who can give us a brife explanation of of selxavg-jk-sess command?
by Zhen Zonglei 08 Apr '08

08 Apr '08

Now we want to do leave-one(run)-out fsfast analysis for feature selection, we hope this command can help us, but not sure. We have not found some useful information in FS wiki and the mailing list. Who can give us some details on this command, especially, its computational process and output?Please help us. Thanks in advance. Zonglei Zhen 2008/4/6, Zhen Zonglei <zonglei.fsl(a)gmail.com>: > > Dear, Dr. Greve: > Sorry for bothering you again. Can you explain us what is function of > selxavg-jk-sess? We have searched its information in FS wiki and mailing > list many times, but nothing is found. Now we want to do leave-one(run)-out > feature selection, we hope this command can help us, but not sure. Please > give us some details on this command, especially, its computational process > and output. Please help us. > > Thanks in advance. > > Zonglei Zhen >

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Restart FreeSurfer
by joel bruss 08 Apr '08

08 Apr '08

Hello- I was running recon-all when my machine croaked. I was on the latter-half of day two and I think (hope) that the process was nearing completion. Is there a command to give to FreeSurfer to start back in the pipeline where the process left off or do I have to do each command separately? Specifically, this was the command I used: recon-all -subjid sub1 -all Is there a flag or comment to check/pick up where I left off or am I out of luck? Thanks for your help. -Joel

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Time-point exclusion failure in selxavg3-sess
by Lionel zorzevic 08 Apr '08

08 Apr '08

Dear Dr Greve, As I tried to introduce time-point exclusions in an analysis, selxavg3-sess returned the following error: ERROR: time points in /.automount/space3/newfspace/070630_METRAPI_TM05/bold/001/spike.txt exceed nframes (91) 91 corresponds to run length in TR (but not in seconds) Just to check, I wrote a TPEF file with numbers _________________________________________________________________ Créez votre disque dur virtuel Windows Live SkyDrive, 5Go de stockage gratuit ! http://www.windowslive.fr/skydrive/

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mri_vol2surf
by Denise M Cote 08 Apr '08

08 Apr '08

Good Afternoon, I am attempting to get a list of cortical thickness statistics on a group of ROIs. The T2 functional data for the subjects was previously analyzed in AFNI, where an ROI mask to be applied to all subjects, was developed. The volume ROI mask was converted from AFNI BRIK to FreeSurfer .mgz format using mri_convert. Recon-all has been run on all T1 anatomical images and fslregister was used to register each subject's anatomical data to the ROI mask. I ran the series of commands below and got results, but the anatomical locations and Talairaich coordinates from FreeSurfer are not close to the values I see in AFNI. How and when should I be aligning the center and orientation of the average subject with the functional mask from AFNI? Here is what I tried, but still did not get accurate results even when mris_info shows the same for both the anatomy and functional mask image files: # cd $SUBJECTS_DIR/MSN.0964.anat/mri mri_convert --apply_transform transforms/talairach.xfm --conform --devolvexfm MSN.0964.anat -ic 0 0 0 orig.mgz orig_Talc000.mgz mri_convert --like orig_Talc000.mgz --conform --devolvexfm MSN.0964.anat -ic 0 0 0 OR_MASK_0005_clust_400_contiguous+tlrc.mgz OR_MASK_Talc000.mgz # mri_info orig_Talc000.mgz >mri_info.orig_Talc000.mgz mri_info OR_MASK_Talc000.mgz > mri_info.OR_MASK_Talc000.mgz # #Using the group ROI mask as a volume dataset in FreeSurfer, I ran the following commands: # # Create average subject cd $SUBJECTS_DIR make_average_subject --out MSNaverage --subjects MSN.0964.anat MSN.0965.anat MSN.0966.anat MSN.0967.anat MSN.0968.anat MSN.0969.anat MSN.0979.anat MSN.0980.anat MSN.1001.anat MSN.1003.anat MSN.1039.anat # # Register functional map to average subject. fslregister --mov $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --s MSNaverage --reg $SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat # # Convert functional mask from AFNI to a surface (both volume and surface belong to the average subject mri_vol2surf --src $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --srcreg $SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat \ --hemi lh --fwhm 6 --out_type mgz --o $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-lh.mgz --trgsubject MSNaverage --nvox $SUBJECTS_DIR/MSNaverage/stats/lh.nvox.dat mri_vol2surf --src $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --srcreg $SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat \ --hemi rh --fwhm 6 --out_type mgz --o $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-rh.mgz --trgsubject MSNaverage --nvox $SUBJECTS_DIR/MSNaverage/stats/rh.nvox.dat # # Map average subject surface to subject MSN.0964.anat surface mri_surf2surf --srcsubject MSNaverage --srcsurfval $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-lh.mgz \ --trgsubject MSN.0964.anat --trgsurfval $SUBJECTS_DIR/MSN.0964.anat/surf/fvol2pialsurf.mgz --hemi lh mri_surf2surf --srcsubject MSNaverage --srcsurfval $SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-rh.mgz \ --trgsubject MSN.0964.anat --trgsurfval $SUBJECTS_DIR/MSN.0964.anat/surf/fvol2pialsurf.mgz --hemi rh # #Create a surface cluster & label for each ROI for subject MSN.0964.anat #generates region & fixed mni (mni2tal.mat) coordinates for each ROI mri_surfcluster --in $SUBJECTS_DIR/MSN.0964.anat/surf/lh.fvol2pialsurf.mgz --subject MSN.0964.anat --hemi lh --annot aparc --thmin 1 --thmax 11 --minarea .01 \ --fixmni --olab lh.pial.surf --sum $SUBJECTS_DIR/MSN.0964.anat/stats/lh.pial.sum.MSN.0964.anat.txt --o lh.pial.clustsurf --ocn lh.vertex.pial.ClusterNum mri_surfcluster --in $SUBJECTS_DIR/MSN.0964.anat/surf/rh.fvol2pialsurf.mgz --subject MSN.0964.anat --hemi rh --annot aparc --thmin 1 --thmax 11 --minarea .01 \ --fixmni --olab rh.pial.surf --sum $SUBJECTS_DIR/MSN.0964.anat/stats/rh.pial.sum.MSN.0964.anat.txt --o rh.pial.clustsurf --ocn rh.vertex.pial.ClusterNum # # Generate statistics for each ROI for each subject set left_rois = ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 ) set right_rois = ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 ) foreach right_roi ( $right_rois ) mri_label2label --srcsubject MSNaverage --srclabel $SUBJECTS_DIR/MSNaverage/label/rh.pial.surf-00${right_roi}.label --trgsubject MSN.0964.anat --trglabel $SUBJECTS_DIR/MSN.0964.anat/label/rh.pial.surf-00${right_roi}.label --regmethod surface --hemi rh mris_anatomical_stats -l rh.pial.surf-00${right_roi}.label -f $SUBJECTS_DIR/MSN.0964.anat/stats/rh.ROI${right_roi}.pial.surfstats -b MSN.0964.anat rh white end foreach left_roi ( $left_rois ) mri_label2label --srcsubject MSNaverage --srclabel $SUBJECTS_DIR/MSNaverage/label/lh.pial.surf-00${right_roi}.label --trgsubject MSN.0964.anat --trglabel $SUBJECTS_DIR/MSN.0964.anat/label/lh.pial.surf-00${right_roi}.label --regmethod surface --hemi lh mris_anatomical_stats -l lh.pial.surf-00${left_roi}.label -f $SUBJECTS_DIR/MSN.0964.anat/stats/lh.ROI${left_roi}.pial.surfstats -b MSN.0964.anat lh white end# Any insight on this process would be greatly appreciated. Thanks very much for your help. Denise M. Cote Sr. Research Assistant Transdisciplinary Research Group Butler Hospital 345 Blackstone Blvd Providence, RI

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problematic pial
by Jamie Hanson 07 Apr '08

07 Apr '08

Hi Freesurfers- I was trying to run freesurfer on a study template and was having major problems with pial surface generation. Orig and Main surfaces seem to be ok, but there are major missing chinks in pial surface. Just to give some background, the template was being using for Diffeomorphic Image Registration, so it is a very unique volume.I know it is likely it is an intensity value issue.I wondered what folks have done previously to correct similar issues? It appears to be across a massive proportion of the brain, so correcting by hand (by altering intensity values seems a bit labor intensive and perhaps questionable in terms of reliability). I also thought of trying to rerun some of the initial preprocessing (autorecon1 + 2) with some more 'expert settings'. Initially, I was running with no skull strip and no n3 flag (b/c the template has already been skull-stripped and massive preprocessed), but was looking for some additional advice and guidance. Any thoughts or suggestions would be greatly appreciated. Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

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Data Discrepancies
by Jared Morton 07 Apr '08

07 Apr '08

I am using Freesurfer to analyze a set of brains of subjects with temporal lobe epilepsy. The brains are being run at two different locations. In addition, the brains at one location have been run on two different computers, with two different freesurfer builds. The problem that I am having is that that each time the data are run, they are markedly different. The differences are substantial, more than should be accounted for by using different versions. In some cases, the differences are from 10-30% off. Has anyone else had this problem? -- Jared Morton M.S. Rosalind Franklin University of Medicine and Science

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