Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

Freesurfer Input Imaging
by Daniel Alejandro Reyna Torres 16 Mar '18

16 Mar '18

Hello, is there any recommendation from Freesurfer for MRI images used during recon-all? i.e., should we use a sagittal MRI, coronal or transversal? For instance, I have one subject with these 3 different orientations. I ran recon-all on the 3 of them and got the results for the reconstruction. I was wondering how can we know which would be more accurate. I have a guess but not sure. Thanks team. Regards, Daniel

3 3

Map mask from volume to surface for small volume correction in surface analyses (using my own template)
by Charlotte Grosse Wiesmann 16 Mar '18

16 Mar '18

Dear freesurfer experts, I would like to restrict my surface analyses (cortical thickness and surface area) to a mask from an fMRI meta-analysis using my own subject-specific template that I created with ANTS. So far, I have used Qdec and wanted to correct for cluster size running the Monte Carlo (MC) simulation on my own template. Now I would like to restrict the simulation to my mask to do a small volume correction in my regions of interest. I mapped the mask to my own template (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask to the surface space to run the MC simulation on my own template within this mask? I was planning to do: mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z --surface my_template ?h --nreps 10000 --mask mymask.mgz How do I get mymask.mgz in the correct space for this? And can I continue using Qdec or do I have to use glmfit for these analyses? In addition: is it also possible to do a small volume correction using FDR rather than cluster-size correction? Thanks for your help! Charlotte

3 6

Creating ROI on the functional map
by Sarah Cole 05 Mar '18

05 Mar '18

Hi, I was wondering if this method is still applicable in version 6 https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs I cannot seem to find any of the options for creating an ROI. Thank you, S

2 4

Novice have a problem
by shilin18 05 Mar '18

05 Mar '18

Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage folder to the SUBJECT_DIR folder and run recon-all … -qcache it will go through. But I think something is missing because in the surf folder, there are no *h.pial.outer_smoothed files created. I really need the files to go forward. Thanks. Reporting on 70 segmentations Using PrintSegStat mri_segstats done /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/label INFO: fsaverage subject does not have uptodate *rhinal labels! \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n #-------------------------------------------- #@# BA_exvivo Labels lh Tue Feb 27 02:44:34 PST 2018 \n mri_label2label --srcsubject fsaverage --srclabel /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject SHICEP_S15_84_KG --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n No such file or directory mri_label2label.bin: could not open label file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srclabel = /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SHICEP_S15_84_KG trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label Darwin Lin.local 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 recon-all -s SHICEP_S15_84_KG exited with ERRORS at Tue Feb 27 02:44:34 PST 2018 For more details, see the log file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

3 2

TRACULA registration
by Gabriela Longo 28 Feb '18

28 Feb '18

Hi, I processed some subjects in TRACULA for a longitudinal evaluation. I registered all of them in the MNI template (set doregmni = 1 set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz). I checked the registration of my dtifit_FA.bbr.nii.gz with the MNI of all subjects. However, when I performed the group analysis, I got more NaN than expected and I checked the images and the results are outside the MNI template (I am sending a picture). I went back and checked the registration of the paths. Despite the dtifit_FA.bbr.nii.gz is correctly registered in the MNI, the paths aren't. I am struggling here to find solutions. I really appreciate any insight to help me to solve this issue. Thanks in advance, Gabriela Longo [image: Imagem inline 2]

2 19

mri_segstats - CTABWriteFileASCII; could not open file for writing
by Yash Patel 28 Feb '18

28 Feb '18

Hello FreeSurfer experts, I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" Whenever I try, I receive the following error (in error.log file); CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file The output in the command prompt is below: cmdline mri_segstats --annot brno/661A.long.024ns lh aparc --i vol2surf/661A.v2s.0.5pf.mgh --sum stats/661A.05pf.sum --id 1001 --id 1002 --id 1003 --id 1005 --id 1006 --id 1007 --id 1008 --id 1009 --id 1010 --id 1011 --id 1012 --id 1013 --id 1014 --id 1015 --id 1016 --id 1017 --id 1018 --id 1019 --id 1020 --id 1021 --id 1022 --id 1023 --id 1024 --id 1025 --id 1026 --id 1027 --id 1028 --id 1029 --id 1030 --id 1031 --id 1032 --id 1033 --id 1034 --id 1035 --ctab-default sysname Darwin hostname ypatel-BYOD.local machine x86_64 user ypatel UseRobust 0 Constructing seg from annotation Reading annotation /Users/ypatel/Documents/brno/661A.long.024ns/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing No such file or directory CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab Interestingly, I ran the SAME code a few weeks ago, and everything worked fine. Somehow something has changed. I also made sure I have permission to /tmp Please let me know if you guys have a suggestion, Thank you Yash

2 4

Fwd: Freeview update on Mac
by Sarah Cole 28 Feb '18

28 Feb '18

Great! Thank you so much, Andrew. I downloaded the updated Freeview. I am still wondering how to draw an ROI on the surface in Freeview. I don't have the options. Could you please let me know what command you are running to get the Freeview? I am having the updated version Jan 2018. Thanks, Sarah On Tue, Feb 27, 2018 at 11:40 AM, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote: > Hi Sarah, I updated the wiki page. We actually just put up a standalone, > dev freeview app today. > > best > Andrew > > > On February 27, 2018 at 11:38:57 AM, Sarah Cole (coleashley00(a)gmail.com) > wrote: > > Hi Doug/Zeke, > > Could you please update the page for freeview update on Mac- if it is > available. > > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > > > Thanks, > > S > _______________________________________________ > 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. >

2 1

Resolution limits of FLAIR/T2w for effective pial refinement
by Christopher Markiewicz 28 Feb '18

28 Feb '18

Hi all, I wonder if people have any data (or anecdotes - I'm not picky) with regard to how high of resolution T2w or FLAIR images need to be in order to be useful for FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5 mm^3) FLAIR images could be tried, but might hurt more than help, and I'm wondering if there's a suboptimal-but-still-useful range somewhere in between. For the record, this isn't a question of what scan parameters are recommended, but rather is in the context of data that's already been collected, which I would like to preprocess as well as possible. So, at what resolutions would you recommend (a) completely ignoring T2w/FLAIR images; (b) including T2w/FLAIR images that pass QC; (c) trying and seeing? Do these answers change at all with T1w resolution? -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University

3 2

Images fail to convert
by Cheryl McCreary 28 Feb '18

28 Feb '18

Dear Experts, I am trying to process a some T1 data through FreeSurfer 5.3.0, but it seems to fail during the first format conversion step. This data is from a multicenter study so I am not familiar with the acquisition details although the images visually look ok. Any suggestions? Thanks, Cheryl -- Cheryl McCreary, PhD MR Research Manager University of Calgary Ph: 403 944 8781 or 403 210 6258

2 1

missing '*h.pial*' files, cannot find fseverage folder.
by shilin18 28 Feb '18

28 Feb '18

Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage folder to the SUBJECT_DIR folder and run recon-all … -qcache it will go through. But I think something is missing because in the surf folder, there are no *h.pial.outer_smoothed files created. I really need the files to go forward. Also, are there ways to manually generate *h.pial-outer-smoothed and other related files, so as to accomplish the final step for iElvis if the *h.pial-outer-smoothed files and a bunch of *h.pial* files are missing? Thanks. Reporting on 70 segmentations Using PrintSegStat mri_segstats done /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/label INFO: fsaverage subject does not have uptodate *rhinal labels! \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n #-------------------------------------------- #@# BA_exvivo Labels lh Tue Feb 27 02:44:34 PST 2018 \n mri_label2label --srcsubject fsaverage --srclabel /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject SHICEP_S15_84_KG --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n No such file or directory mri_label2label.bin: could not open label file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srclabel = /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SHICEP_S15_84_KG trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label Darwin Lin.local 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 recon-all -s SHICEP_S15_84_KG exited with ERRORS at Tue Feb 27 02:44:34 PST 2018 For more details, see the log file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/scripts/recon-all.log To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

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Freesurfer February 2018