Freesurfer

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30084 discussions

mysterious fsgd format error (not the end of line problem)
by Joseph Dien 06 Mar '16

06 Mar '16

Hi, I’m having an fsgd error that has totally stumped me. I’m trying to run the following command to compute the second level statistics: mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C normAcc.mtx I get the error message: Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white gdfReadHeader: reading RPA-accGT.fsgd FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title I used the utility flip to make sure the file was in UNIX format (with linefeeds). I then double-checked by reading in the binary codes with Matlab’s fread and directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed). Here is the contents of the fsgd file. GroupDescriptorFile 1 Title RP1 Class Main Variables LogoAcc NormAcc OrthAcc PhonAcc Input RPA903 Main 0.75 0.79 0.77 0.62 Input RPA906 Main 0.81 0.81 0.83 0.74 Input RPA907 Main 0.87 1 0.84 0.83 Input RPA908 Main 0.91 0.93 0.95 0.89 Input RPA909 Main 0.74 0.95 0.72 0.72 Input RPA910 Main 0.85 0.96 0.81 0.79 Input RPA912 Main 0.75 0.78 0.73 0.73 Input RPA914 Main 0.7 0.85 0.83 0.81 Input RPA915 Main 0.85 0.89 0.75 0.83 Input RPA916 Main 0.84 0.92 0.87 0.72 Input RPA917 Main 0.83 0.93 0.92 0.83 Input RPA918 Main 0.87 0.91 0.79 0.85 Input RPA919 Main 0.86 0.96 0.91 0.88 Input RPA920 Main 0.84 0.92 0.87 0.84 Input RPA921 Main 0.87 0.92 0.88 0.85 Input RPA922 Main 0.8 0.9 0.9 0.72 What’s really driving me to distraction is that a previous version of this file (with a different set of participants) works fine. I’m attaching both. RPA-accGT.fsgd does not work and RPA-acc.fsgd does work. Using Matlab’s fread, the first 85 characters (first four lines) of both files are identical. I’m running on OS X 10.11.3. I’m using FSFAST 5.20. Matlab 2015b. Any help would be greatly appreciated! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07(a)mac.com Cell Phone: 202-297-8117 http://joedien.com

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Re: [Freesurfer] T2pial shrinks pial surface
by Matt Glasser 06 Mar '16

06 Mar '16

What FreeSurfer version are you using? Very small changes to the input images (e.g. a different random see for FreeSurfer) may be able to kick mris_make_surfaces out of that bug, though perhaps Bruce has fixed it. Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Chris Adamson <chris.adamson(a)mcri.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Sunday, March 6, 2016 at 6:14 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] T2pial shrinks pial surface The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children¹s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adamson(a)mcri.edu.au www.mcri.edu.au <http://www.mcri.edu.au/> <https://www.facebook.com/MurdochChildrensResearchInstitute> <https://twitter.com/MCRI_for_kids> <http://instagram.com/murdoch_childrens> <http://www.youtube.com/user/MurdochChildrens/videos> <https://donate.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. PPlease consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ _______________________________________________ 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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Deflate surface
by marmaduke woodman 06 Mar '16

06 Mar '16

Hi I would like to resample the cortical surface on the sphere at a lower resolution, and then deflate the surface to its folded form. Is this something which can be done using the inflated surface that FS generates? Thank you, Marmaduke

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Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!
by Ankita Chatterjee 06 Mar '16

06 Mar '16

Thank you for the pointer Woo-Suk. So to do that, I just do an EXPORT PATH on Matlab? I am not very familiar with linux... Thanks! Ankita

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TRACULA Adding a new tract to the finished analysis
by denizzgursel 05 Mar '16

05 Mar '16

Dear Anastasia and Tracula users, I ran the longitudinal pipeline of Tracula with my subjects and I finished without error. However, I just realized now that I only added cingulum gyrus ending but not the angular bundle. I am interested in tracts that passes through hippocampus so angular bundle should be included. I would like to add this tract to the analysis. My question is, do I have to re-run everything from scratch? Is it possible to run just one tract? Do I have to do the preprocessing again? I really hope there is a way around this as I spent very long time finishing the analysis. Thank you for your help. Best regards, Deniz Gürsel

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Generating Masked Aseg Segmentation Volumes
by Sarah Blankenship 05 Mar '16

05 Mar '16

Hi Freesurfer Team, I'm attempting to calculate the volume of hippocampal subfields (e.g., CA1-3, DG) in the anterior (head), middle (body), and poster (tail) subregions of the hippocampus. I have manually determined the boundaries for head/body/tail using standard anatomical landmarks and included these updated labels in the aseg files. I am attempting to use those (head/body/tail) volumes as masks when generating the hippocampal subfield (CA1-3, DG) volumes. Could you confirm that these are the correct steps to this end? *Note.* Based on the prior literature, the asegs were ac-pc aligned in AFNI to determine unbiased boundaries for head/body/tail. mri_binarize --i aseg_acpc_antpost.mgz --match 91 --o Lhead_mask.nii > #LHead=label 91 > mri_segstats --seg lh.hippoSfLabels-T1-T1T2.v10.1mm_acpc.nii --mask > Lhead_mask.nii --excludeid 0 --pv norm_acpc.nii --sum > ../stats/substats_lhead The outputs appear reasonable (i.e., the volumes generated by mri_segstats with the mask are smaller than without the mask), but I wanted to ensure that this is the appropriate method to generate what I'm looking for. Thank you in advance for your help! Sarah

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recon-all -lgi issue with MATLAB Student version
by Ankita Chatterjee 05 Mar '16

05 Mar '16

Attached is my recon-all.log file

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recon-all -lgi issue with MATLAB Student version - Help!
by Ankita Chatterjee 05 Mar '16

05 Mar '16

Hello FS experts, I am a bit stuck and was hoping for some advice! I am using Matlab Student version for my research and was trying to determine local gyrification index on some samples that I have processed via the recon-all -all step. When I run recon-all -lgi on my subject, it starts up, is able to access MATLAB, but then gives an error >> Undefined function or variable 'make_outer_surface'. Am I missing a package from the MATLAB student version? How do I solve this? Any help will be greatly appreciated!!! Ankita

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recon-all and local Gyrification Index
by Ankita Chatterjee 05 Mar '16

05 Mar '16

Hello, I ran several recon-all processes on raw T1 MRI data. I was trying to run recon-all -lgi as per the instructions from this paper - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/ but it fails with an error that Matlab is required. So, my question is if local GI is already computed by running recon-all? Or, do I need to get MatLab? Since I don't have MatLab, any other workarounds? Thanks! Ankita

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mkbrainmask-sess and inorm-sess
by Ji Won Bang 04 Mar '16

04 Mar '16

Dear. Freesurfer experts. Hi. How are you? It might be very naive question. When using version 4.5.0 I used the command: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino However under the version 5.3.0, mkbrainmask-sess does not have -funcstem. May I use -maskstem instead of -funcstem? If so, after that, I tried: inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd bold_retino However, it complains that: ERROR: cannot find /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain You may need to run preproc-sess or mkbrainmask-sess to create a brain mask Could you please help? Thank you very much. Best, Ji Won

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