Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30065 discussions

installtation error
by 水墨丹青 07 Aug '17

07 Aug '17

TO: freesurfer(a)nmr.mgh.harvard.edu FROM: fsuser(a)worlduniversity.edu SUBJECT: installation error error: there is no setupfreesurfer.sh file Hello FreeSurfer Developers, I'm attempting to install freesufer on my computer(linux ubuntu 14).But there is on setupfreesurfer.sh file.I can find a setupfreesurfer.csh file on installation directory.I think I should install it using bash rather than tcsh.Thank you every much! I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: CentOS release 6.7 (Final) 3) uname -a: Linux ubuntu 14.0.4 LTS 4) recon-all.log: see attached

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Need Urgent Help!! Regarding FreeSurfer Installation
by Tabassum, Ruchira 05 Aug '17

05 Aug '17

Hi, I need Freesurfer for my windows OS. Is there any windows version of FreeSurfer? Please let me know ASAP. Kind Regards Ruchira Tabassum

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Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation
by Matt Glasser 05 Aug '17

05 Aug '17

No. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Tabassum, Ruchira" <Ruchira_Tabassum(a)student.uml.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Saturday, August 5, 2017 at 12:22 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation Hi, I need Freesurfer for my windows OS. Is there any windows version of FreeSurfer? Please let me know ASAP. Kind Regards Ruchira Tabassum _______________________________________________ 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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Co-ordinate systems in FS
by Martin Juneja 04 Aug '17

04 Aug '17

Hi FreeSurfer experts, I am trying to correlate my behavioral data with whole brain cortical measures using cortical measures as IVs and behavioral data DV. Somehow the significant clusters I get from cortical thickness, area and volume are in MNI co-ordinates but significant clusters from local gyrification-behavioral data are in Talairach co-ordinates. I used identical procedures to preprocess my data but still I am getting my results in different co-ordinate systems (thickness, volume, area in MNI and gyrification in Tal). I would really appreciate any help. MJ

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label2annot issue
by Redwan Maatoug 04 Aug '17

04 Aug '17

Hi all, So my issue is the following : I have 112 mgh files. (They come from the Yeo 17 Network atlas (we split the atlas in smaller regions). I have extracted the coordinates with : mri_surfcluster (playing with the thmin option) mri_vol2label and then I have used mri_label2annot with my own color lookup table to combine the 112 files into 1 file. (I have played with --noverbose, --maxstatwinner) When I try to display, I have the feeling that there is some overlapping because what tksufer dispays, is not very relevant and it is spotty. I have attached some screenshots Thank you very much for your help, Redwan

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Optseq2 onset times
by Ruthie Shaffer 04 Aug '17

04 Aug '17

Hi, I’m using Optseq2 to generate stimulus / jitter schedules, and, depending on the TR used, in the output timing files I see several event onset times very close to the correct time, but slightly off (for example, something like 124.7999, instead of 124.8). I’ve used the following command to generate timing files: optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 --nkeep 6 --o CRtiming.2017 --nsearch 100000 --tnullmin 0 --tnullmax 6.4 Should I be concerned about optimal onset times that are slightly off from the actual possible onset times based on the TR, or is it correct to assume it should be 124.4, instead of 124.4001 or 125.8, instead of 125.7999, for example? Thank you in advance for any help on this! Best wishes, Ruth Shaffer

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Pineal gland volume?
by Rotem Saar 04 Aug '17

04 Aug '17

Dear Freesurfer experts, I wondered if its possible to extract the volume of the *pineal gland* using the basic cortical + sub-cortical segmentation (recon-all)? I could not find the volume of this ROI in the output. If the volume output for this ROI is available - please guide me where to look (maybe I missed it?) If not - does manual ROI drawing and following,volume calculation is possible using freesurfer? Thanks ! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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Re: [Freesurfer] output with input matrix size and referential
by pierre deman-kibleur 04 Aug '17

04 Aug '17

yes, it's what i wanted to say. On Aug 2, 2017 17:46, "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> wrote: what do you mean by referential? the coordinate system of the vertex coords? On 8/2/17 4:49 AM, pierre deman-kibleur wrote: Hi, Is it possible to have the gifti output in the same referential as the orig nii file as well ? I tried mris_convert lh.white lh.white.gii -rl mri/orig/001.mgz but mris_convert doesn't have the -rl option. Regards, Pierre On Wed, Aug 10, 2016 at 2:40 PM, Iglesias, Eugenio <e.iglesias(a)ucl.ac.uk> wrote: > You can always run mri_convert with the -rl (“reslice like”) flag to > achieve this. Something like: mri_convert input.mgz output.mgz -rl > reference.mgz -odt float > If it’s a segmentation volume, you should add -rt nearest, in order to use > nearest neighbor interpolation. > Cheers, > Eugenio > > Juan Eugenio Iglesias > Translational Imaging Group > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > On 10 Aug 2016, at 13:31, pierre deman <deman.pierre(a)gmail.com> wrote: > > Hello, > > I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield > etc ... > in a matrix with the same size as the input of recon-all (and not the > cubic matrix 256x256x256) and with the same orientation. > > what is the best way to do it ? > > Cheers, > Pierre > > -- > DEMAN Pierre > Mobile : +33 7 82 57 80 94 <+33%207%2082%2057%2080%2094> > _______________________________________________ > 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. > > > > _______________________________________________ > 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. > > -- DEMAN Pierre Mobile : +33 7 82 57 80 94 <+33%207%2082%2057%2080%2094> _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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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Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing
by Elijah Mak 03 Aug '17

03 Aug '17

Hi ZK, Thanks. It is great news! I would like to report the following. asegstats2table seems to be acting strangely. File "/Applications/freesurfer_b6/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Even typing asegstats2table --help leads to the same error message. It was not found in a prev dev built or in 5.3. Thanks. Also, not sure if it's placebo, but freeview seems to be running quicker now. Best Wishes, Elijah

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Medial Surface Problem
by Bronwyn Overs 03 Aug '17

03 Aug '17

Hi mailing list, I am currently processing a longitudinal image and have come across a problem at the medial surface in the long image (step 3). As you can see in the attached image, the rh medial surface has been significantly overestimated and extends into the lh surface. This error showed up only in only 1 of the 2 long images for this subject, and both the time-point images and the base are perfectly fine. Do you know why this is happening? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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