Freesurfer May 2014

freesurfer@nmr.mgh.harvard.edu

139 participants
206 discussions

Paradigm files
by Emily Boeke 12 May '14

12 May '14

Hi Freesurfers, I am doing some analyses for an experiment where paradigm files were automatically generated by Matlab during stimulus presentation. The script was designed to make paradigm files for an older version of freesurfer, so the files only have 2 columns. I am going to adjust these files so that they can be read by FS 5.3 (add in the extra columns needed). I noticed that there is a line for each TR as opposed to for the onset of each stimulus, for example, it looks something like this: 0 2 2 2 4 2 6 2 8 1 10 1 12 1 14 3 16 3 instead of 0 2 8 1 14 3 Is this a problem? Can I leave it as is and then just add a column of 2s and a column of 1s? Thanks! Emily

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2x3 DODS analysis question?
by Khadka, Sabin 12 May '14

12 May '14

Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DODS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low Class MaleGroup2Medium Class MaleGroup2High Class FemaleGroup1Low Class FemaleGroup1Medium Class FemaleGroup1High Class FemaleGroup2Low Class FemaleGroup2Medium Class FemaleGroup2High Variables Age normVol Input SUB001 MaleGroup1Low 18 0.4 . . . And also my contrast files as Group1Group2.mtx [1 1 1 -1 -1 -1 1 1 1 -1 -1 -1]/3 MainEffectState.mtx 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 HighvLow.mtx -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 HighvMed.mtx 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 GroupxState-interaction.mtx 0.5 -0.5 0 -0.5 0 0.5 0.5 -0.5 0 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 I'd appreciate if anyone could please let me know that my design is correct. Thanks for help. -Sabin

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Error running recon-all on hpc computers
by Natalie Garcia 12 May '14

12 May '14

Hi all, I'm trying to run recon-all on some data using one of the hpc clusters at my institution using FreeSurfer v. 5.3.0. I've used 4.5.0 without a problem but I'm trying to rerun the data with the new version. I keep getting this error (FreeSurfer's log file is attached here) regarding the mni/bin folder. Could this be an error on their end? Not sure if maybe 5.3 wasn't installed correctly on the hpc machines. Any help is really appreciated! Thanks, Natalie -- Natalie V. Garcia Graduate Fellow, Cognitive Neuroscience Department of Psychology The Pennsylvania State University 423 Moore Building University Park, PA 16802 nvg109(a)psu.edu

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bbregister to register a .annot file to MNI space
by Nathan Hutcheson 12 May '14

12 May '14

Hello, I am trying to use bbrestier to take an .annot file of a particular structure and register it to MNI space. I want to be able to use one of the FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and do a fMRI BOLD extraction in FSL in MNI space. Below is the command I used and the error message I am getting. Please let me know if what I am doing makes any sense or if I am way off base. Input > bbregister --s fsaverage --mov > /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label --t1 > --init-fsl --reg register.dat > > Output > mkdir: cannot create directory `./tmp.bbregister.6489': Permission denied > > Log file is register.dat.log > > register.dat.log: Permission denied. > Take care, Dr. Nathan Hutcheson Postdoctoral Researcher University of California Los Angeles Semel Institute 760 Westwood Plaza C8-202 Los Angeles, CA 90024 T: 770.841.1694 nathanhutcheson.com <http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46>

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A question about installation
by 木村一皓 12 May '14

12 May '14

Hi, I would like to install "Freesurfer," but I have a problem. I now only have a PC running Windows OS. So I am wondering if I could use "Freesurfer" by windows.(say in "VMware Player") Or should I buy Macintosh or somtehing because of memory problems? Sorry for my really novice question, Ikko Kimura

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get the max value
by charujing123 11 May '14

11 May '14

Hi all I want to get the maximum value in one surface-based file. How can I make it? Thanks. All the best. Rujing Zha 2014-05-11 charujing123

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a question on flat surface
by peng 10 May '14

10 May '14

Hi Freesurfers, I have tried to obtain a flat surface as described by the upper part (full cortex) of the following page: http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch However, I failed to load the results in freeview (it took forever), nor can I read in matlab with read_surf. The error in matlab is as following ====== Error using reshape To RESHAPE the number of elements must not change. Error in read_surf (line 77) vertex_coords = reshape(vertex_coords, 3, vnum)' ; ====== Thus I suspect in the newly generated surface, the number of vertices in the header does not meet that indicated by the data. I did sth wrong. Questions: 1 Is this webpage still up-to-date or I shall try something new to flatten the surface? 2 Probably there are "frequently made mistakes" during my manual process, would you please give me a hint? I my case afterwards mris_flatten took 2-3 hours. btw: the inflated surface is OK either checked by freeview or matlab. best Peng

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Re: [Freesurfer] Viewing functional data on the inflated brain
by Sherryse Corrow 09 May '14

09 May '14

Thanks Douglas. Yes, both of those exist. -- Sherryse Corrow, Ph.D. / Postdotoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org On 5/7/14, 6:54 P, "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.du> wrote: >Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > >To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mghharvard.edu/mailman/listinfo/freesurfer >or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > >You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. Re: Viewing functional data on the inflated brain > (Sherryse Corrow) > 2. Re: vertex-wise cortical thickness and whole brain labeling > (Douglas N Greve) > 3. Re: Question about Qdec p-values (Douglas N Greve) > 4. Re: Quesion about lobar volumes (Douglas N Greve) > 5. Re: Viewing functional data on the inflated brain > (Douglas N Greve) > 6. Re: vertex-wie cortical thickness and whole brain labeling > (Bruce Fischl) > 7. Re: aseg.stats volume mismatch (Gabor Perlaki) > 8. Re: aseg.stats volume mismatch (Bruce Fischl) > 9. Covert processed RS time series to MNI152 (Paul Beach) > 10. Re: Quesion about lobar volume (pfotiad(a)nmr.mgh.harvard.edu) > 11. Re: Quesion about lobar volumes (Douglas N Greve) > 12. Re: Quesion about lobar volumes (pfotiad(a)nmr.mgh.harvard.edu) > 13. Re: LOOK FOR HELP! (???) > > >-------------------------------------------------------------------- > >Message: 1 >Date: Wed, 7 May 2014 10:59:55 -0700 >From: Sheryse Corrow <sherryse.corrow(a)eyecarecentre.org> >Subject: Re: [Freesurfer] Viewing functional data on the inflated > brain >To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>>Message-ID: <CF8FC0ED.AE9A%sherryse.corrow(a)eyecarecentre.org> >Content-Type: text/plain; charset="windows-1252" > >Tanks Douglas. We tried that . . . The registration matrix that we need >is not created. Here is the output log file (attache). I am a bit new to >this so I am hoping it has the information you need. After taking a quick >glance at the log file, we noticed there are errors in the log file. > >Step by step, this is what we did after we an recon-all: >Reg-feat2anat ?feat OurFeatDirectory.feat ?subject P209 > >When we open the folder experiment.feat/reg/freesurfer, there is no >anat2exf.register.dat file. However, there is a file called: >anat2exf.register.dat.init. > >Thanks, >Sherryse >-- >Sherryse Corrow, Ph.D. / Postdoctoral Fellow >Human Vision and Eye Movement Lab >Department of Ophthalmoogy & Visual Sciences >UBC/VGH Eye Care Centre >360A-2550 Willow Street >Vancouver, BC, V5Z 3N9 >Tel: 604-875-4111 ext 67672 > >Cell: 604-315-6717 > >sherryse.corrow(a)eyecarecentre.org > > > > > >On 5/6/14, 9:00 AM, "freesurfer-request(a)nmr.mgh.harvard.edu" ><freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > >>Re: Viewing functional data on the inflated brain > >

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nonlinear models in longitudinal analysis
by Jodie Davies-Thompson 09 May '14

09 May '14

Dear Freesurfer experts, I am attempting to do a longitudinal analysis of cortical thickness with 3 timepoints. So far, I have successfully completed the analysis for long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to timepoint 3, and a linear increase for timepoint 1 to 2 to 3. However, I am primarily interested in finding regions which show a) an increase between timepoint 1 and 2, but no difference between 2 and 3, and b) no difference between timepoint 1 and 2, but an increase between 2 and 3. Would the correct way of 'modelling' these two in the qdec file be: a) fsid fsid-base years day1 base 0 day2 base 3 day3 base 3 and b) fsid fsid-base years day1 base 0 day2 base 0 day3 base 3 All the best, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003

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Covert processed RS time series to MNI152
by Paul Beach 09 May '14

09 May '14

Hi Freesurfers, I have several processed resting time series files (processed through AFNI) and I'd like to convert them to MNI space. I have done this successfully for T1Volumes and some ROI masks using mri_convert and tried to use the same code for the resting series. However, I've run into a few issues - namely that the transformation cuts off part of the top of the cortex. My code: *mri_convert -it nii -ot mgz CleanData_RestState.nii.gz CleanData_RestState.mgz* *mri_convert CleanData_RestState.mgz --apply_transform transforms/talairach.xfm \* *-oc 0 0 0 CleanData_RestState_talairach.mgz * *mri_convert CleanData_RestState_talairach.mgz \ cleanData_RestState_talairach.nii.gz* The final time series file, overlayed on the transformed T1Volume, is below. [image: Inline image 1] Any suggestions? How big a problem is this? Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

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Freesurfer May 2014