Freesurfer

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30084 discussions

Pial Surface, total area?
by Guido Orlando Pascariello 21 Dec '15

21 Dec '15

Hi FS Experts I want to get the total area from pia cortex, in order to normalize the parcellations measure. In lh.aparc.statsfile on there is a line: # Measure Cortex, WhiteSurfArea, White Surface Total Area, ****** mm^2 > I've looking for this topic in the lista and I found there is a way to get PialSurfArea. However I wonder if needed to achieve my goal. I mean, why doesn't recon-all measure this area? Is WhiteSurfArea enought to normalice the parcellations? I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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no aseg.stats after recon-all -all?
by Schweren, LJS (med) 21 Dec '15

21 Dec '15

Dear Freesurfer experts, I'm trying to get BrainSeg for 5 subjects. I'm running the following commands: for scan in ... do cd $SUBJECTS_DIR recon-all -all -subjid $scan done It completes recon-all, but with errors. These are the errors: [me@mycomp]$ cat recon-all.error ------------------------------ SUBJECT [mysubj] DATE Thu Dec 17 12:57:00 PST 2015 USER me HOST mycomp PROCESSOR x86_64 OS Linux Linux emotion.ucsd.edu 2.6.18-406.el5 #1 SMP Tue Jun 2 17:25:57 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local/freesurfer/bin/recon-all PWD /[mypathtoSUBJECTS_DIR]/[mysubj]/scripts CMD mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 [mysubj] lh ../surf/lh.sphere.reg /usr/local/freesurfer5/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot [me@mycomp]$ cat error.log GCSAread(/usr/local/freesurfer5/average/lh.DKTatlas40.gcs): could not open file As a result, I don't have any aseg.stats, nor any aparc+aseg files. I ran mri_segstats separately, but then I only get the subcortical volumes, not the totals. If I include the --brain-vol-from-seg flag, it errors again, saying: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz --brain-vol-from-seg --ctab /usr/local/freesurfer5/FreeSurferColorLUT.txt --excludeid 0 --sum /[mypathtoSUBJECTS_DIR]/scripts/[mysubj].aseg.sum sysname Linux hostname mycomp machine x86_64 user me UseRobust 0 Loading /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz Getting Brain Volume Statistics MRISread(/[mypathtoSUBJECTS_DIR]/(null)/surf/lh.white): could not open file No such file or directory I'm hoping you can help me! My goal is to get just BrainSeg for these subjects, I don't need the other outcomes. So if there is a work-around I would be happy to hear. Thank you for your help! All my best, Lizanne ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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R: R: Re: R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 21 Dec '15

21 Dec '15

I have run mri_fdr --help but I obtained this warning: /Applications/freesurfer/bin/mri_fdr: Permission denied. I would also ask you if is possible to threshold the FDR map (p<0. 05), eliminating clusters < 5 voxels. Thanks Stefano >>----Messaggio originale---- >>Da: greve(a)nmr.mgh.harvard.edu >>Data: 11-dic-2015 20.23 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST >> >>$FREESURFER_HOME/bin >> >>On 12/11/15 2:08 PM, stdp82(a)virgilio.it wrote: >>> Thanks, in which folder I should put this file? >>> >>> Stefano >>> >>> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 7-dic-2015 19.23 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] FDR in FS-FAST >>>> >>>> >>>> >>>> On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >>>>> Hi list, >>>>> I have two concerns, please: >>>>> 1) It is possible to apply FDR correction on rs-fMRI seed based >>>>> analysis by FS-FAST? If yes, I can I do it? >>>> try this binary >>>> ftp://surfer.nmr.mgh.harvard. >edu/transfer/outgoing/flat/greve/mri_fdr >>>>> 2) I have apply the FS guidelines and I have used Montecarlo >>>>> correction with threshold at 1.3 but in the within group analysis >>> the >>>>> clusters are very large. In the guide I read examples with a >>> threshold >>>>> at 3. Is there a specific reason? >>>> There is not a hard-and-fast criteria for the voxel-wise >threshold. 3 >>> is >>>> fine as is 1.3 >>>>> Thanks >>>>> >>>>> Stefano >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/ >>>> _______________________________________________ >>>> 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 >>> >>> >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://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 >

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Z-score from .label
by stdp82＠virgilio.it 21 Dec '15

21 Dec '15

Hi list, I would like to extract the mean z-score from a roi.label in each subject after FS-FAST (rs-fMRI seed based).How can I do? Thanks Stefano

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segmentation fault (core dumped)
by Fengji Geng 21 Dec '15

21 Dec '15

Dear freesurfer developers and users, I encountered an error as 'segmentation fault (core dumped)' when I run 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'. Attached is the error log. The version of freesurfer is 'freesurfer-Linux-centos6_x86_64-dev-20151006'. Here goes our server information: LSB Version: :base-4.0-amd64:base-4.0-ia32:base-4.0-noarch:core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch Distributor ID: RedHatEnterpriseServer Description: Red Hat Enterprise Linux Server release 6.6 (Santiago) Release: 6.6 Thank you in advance for your help. ----- Fengji

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Qdec
by Caroline Beelen 21 Dec '15

21 Dec '15

Dear Freesurfer experts, I just started using Freesurfer for performing MRI (T1)- group-based ROI analysis and managed to go through the first recon-all processing stream and making few manual edits. Then I followed first steps of the Qdec -procedure. However, there is a separate section on ROI-analysis as well. Are they complementary or not (which one to follow best)? I tried both. However, at the Qdec section I got lost at creating the table: how to know volumes of pre-specified structures? At the ROI-section I got lost at the point of adding labels to the average subject: cd $freesurfer (directory) mri_label2label \ --srcsubject avgsubject \ --srclabel avgsubject/label/lh.BA45.label \ --trgsubject A06_T1 \ --trglabel A06_T1/label/lh.BA45.label \ --hemi lh \ --regmethod surface (followed the example) I got the error of: subject_dir .../freesurfer Freesurfer_home .../freesurfer Loading source lab: 'no such file or directory'...etc. ... ERROR reading lh.BA45.label. What am I doing wrong? Thank you very much for your response in advance. Kind regards, Caroline

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Help importing files from a previous SPM analysis
by Luis Fernado Silva Castro de Araújo 20 Dec '15

20 Dec '15

Hi all, I am just starting to learn to analyse neuroimaging data. So these are my first steps with FreeSurfer. I apologize if the question is too basic to the mail list. I set myself the goal of finding volumes for several areas in a dataset from the lab I am working on, but I got stuck very early on the exercise. As far as I understood by reading the Tutorials, all the magic happens with the recon-all command, right? But it seems that it requires a specific directory structure to run properly (the FSFAST structure <http://freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct>). The problem is that the dataset for my exercise is organized in a different structure. It was previously analysed in SPM. The structure is as follows. For patients: /experiment/patients/A.o/ and for controls: /experiment/controls/A.o/ Within each directory there are .hdr, .img, .mat and .mask files for each observation, which was obtained in two different times. So the naming of the files have the following order: experiment_subjectnumber_time1.img and for the second acquisition reads: experiment_subjectnumber_time2.img The same with all the before mentioned extensions (hdr, mat, mask). It seems that in the FreeSurfer workflow the command unpacksdcmdir <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData> is used to extract data from the nii and dicon types and organize them in the FSFAST structure. Can it be used on directory structures like the one I have? Or is there anyway of automating the conversion from this structure into the FSFAST’s? Thank you, luis

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Meaning of resample type in mri_convert - Repost
by Gronenschild Ed (NP) 20 Dec '15

20 Dec '15

Hi FreeSurfer developers, Can you please provide information on the resample types "interpolate" and "weighted" which can be specified with option -rt in mri_convert? Cheers, Ed

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Masks on tksurfer
by stdp82＠virgilio.it 18 Dec '15

18 Dec '15

Hi list, I would like to make a mask of a significant cluster after FDR correction on sig.mgz (FS-FAST analysis). I'm using tksurfer and its options (custom fill, new label from marked) but I have some difficulties to save the mask. Could you suggest me a reference/guide page, please? Thanks Stefano

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move annotations across hemispheres
by Peggy Skelly 18 Dec '15

18 Dec '15

Hi, I am attempting to move an annotation file from the right to left hemisphere. I have run xhemi registration with: surfreg —s $subj —t fsaverage_sym —lhrh surfreg —s $subj —t fsaverage_sym —lhrh —xhemi The annotation file is rh.myclusters.annot in the $subj/xhemi/label subdirectory. I've tried using both mri_surf2surf and mris_apply_reg: mri_surf2surf --srcsubject s1315_base/xhemi --sval-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --tval $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --trgsubject s1315_base --srchemi rh --trghemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsurfreg fsaverage_sym.sphere.reg mris_apply_reg --src-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --trg $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --streg $SUBJECTS_DIR/s1315_base/xhemi/surf/rh.fsaverage_sym.sphere.reg $SUBJECTS_DIR/s1315_base/surf/lh.fsaverage_sym.sphere.reg --no-rev I've tried mris_apply_reg with and without the '--no-rev' flag. The output from each of these commands is the same: the clusters are on the medial aspect of the LH. They were clusters in the supramarginal and temporal regions on the RH, so I was expecting them to be in the same regions on the LH. Thanks, Peggy

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