Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

label to vol
by francesca bottino 27 Jan '17

27 Jan '17

Dear FS's experts, I have this problem: I want transform a volume file .nii in surfaces files .label. I had tried the command cor2label but I don't know very well how to use it. Please help me. Tnks ________________________________ Da: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> per conto di freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Inviato: giovedì 26 gennaio 2017 18.00 A: freesurfer(a)nmr.mgh.harvard.edu Oggetto: Freesurfer Digest, Vol 155, Issue 41 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.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - mail.nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ... 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. Longitudinal stream with v6 but cross with v5.3 (Matthieu Vanhoutte) 2. Re: Hippocampal Subfields Segmentation Error (Iglesias Gonzalez, Eugenio) 3. Re: longitudinal tracula error (Yendiki, Anastasia) 4. Re: freesurfer 6.0 with some of the analyses (Rizvi, Batool) 5. Re: Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (Lilla Zollei) 6. Re: freesurfer 6.0 with some of the analyses (Adam Martersteck) 7. Re: freesurfer 6.0 with some of the analyses (Iglesias Gonzalez, Eugenio) ---------------------------------------------------------------------- Message: 1 Date: Thu, 26 Jan 2017 09:58:30 +0100 From: Matthieu Vanhoutte <matthieuvanhoutte(a)gmail.com> Subject: [Freesurfer] Longitudinal stream with v6 but cross with v5.3 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAF6uKJSd96orkeH+WWX5T6jz3xeYtTNiJ80i96C_5do1L8CWqA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear FS's experts, I have run all my cross with v5.3 and hesitate to run all longitudinal process with v6. Does that make sense and will improve the process or would it be risky to do this ? Many thanks for your lights ! Best regards, Matthieu

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Confusion while planning analysis on QDEC
by Vikas Bandalli 27 Jan '17

27 Jan '17

Dear Freesurfer developers, I had a small confusion while performing a paired analysis. An analysis is to be performed to examine or analyze the structural differences between two group 'Control' and 'Patient' subjects. If my study is age and sex matched, say there is a control with same age and sex for every patient, How should I plan my analysis on QDEC, I am currently following this pattern, *Fixed fatcor :- Diagnosis (normal or patient)Continous factor* :- *Age * *Nuisance factor *:- *Total ICV* Is this a correct design? or should I add *sex * to the *fixed factor,* i.e, *fixed factor :- Diagnosis & Sex * How will my analysis vary with and without using sex as fixed factor ? Which is the correct design? Thank you very much in advance. Regards, Vikas Bandalli Raju -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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Registration: Variable Must Begin with a Letter Error
by Anderson Napolitano 27 Jan '17

27 Jan '17

?Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and removing the spaces all together doesn't seem to resolve the said error.

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Hippocampal Subfields Segmentation Error
by Michel Hu 27 Jan '17

27 Jan '17

Dear Freesurfer Developers, For my research I'm trying to run the hippocampal subfield segmentation analysis however, I keep running into the following error. I tried to solve it by myself however I had no luck ( I tried by removing the exec flag from the files ). I'm using the following sofftware Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Ubuntu: 14.04.5 LTS WIndows 10 michel@-:~$ recon-all -s bob -hippocampal-subfields-T1 Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 /usr/local/freesurfer/subjects/bob/scripts/recon-all.log Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy' #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects left See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 2017 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 /usr/local/freesurfer bob /usr/local/freesurfer/subjects right See log file: /usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while loading shared libraries: libut.so: cannot enable executable stack as shared object requires: Invalid argument Started at Tue Jan 24 13:43:45 STD 2017 Ended at Tue Jan 24 13:43:47 STD 2017 #@#%# recon-all-run-time-hours 0.001 recon-all -s bob finished without error at Tue Jan 24 13:43:47 STD 2017 done Sincerely, Michel

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mri_label2label problem
by Bronwyn Overs 26 Jan '17

26 Jan '17

Hi Mailing list, I have been running the mri_label2label command and have encountered a problem with the newly generated label. The command I am running is as follows: mri_label2label --srclabel "$SUBJECTS_DIR/fsaverage/label/lh.sm20.lme.test.B2-0001.label" --srcsubject fsaverage_mod --trglabel "Test.label" --trgsubject “sub003" --regmethod surface --hemi lh When I visualise the original label there is a distinct temporal ROI outlined. However, when I load the label for my individual subject there is no temporal ROI outlined, instead I see numerous widely dispersed vertices highlighted across the whole surface of the cortex. Can you identify what the issue is? I have attached images that show the input and output labels overlayed on an inflated surface. 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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Matlab Runtime
by stdp82＠virgilio.it 26 Jan '17

26 Jan '17

Hi list,please see the error reported below.ThanksStefano curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&am…" -o "runtime2012b.tar.gz" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0Warning: Failed to create the file runtime2012b.tar.gz: Permission denied 0 290M 0 985 0 0 3211 0 26:23:33 --:--:-- 26:23:33 3208

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surface based analysis
by John Anderson 26 Jan '17

26 Jan '17

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Surface space ICA
by David Baric Parker 26 Jan '17

26 Jan '17

Hello! I tried to look through the history but couldn't seem to find exactly what I was looking for. Is there a recommended way to run ICA on vertex data? For example, I've transformed my raw fMRI data to surface space using fsfast, and would like to extract group level IC's from this data. Thanks! -David

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Voxel intensities and aseg edits
by Tamara Tavares 26 Jan '17

26 Jan '17

Hello, I have two questions which I was hoping to get some help with. (1) I was wondering whether there was a intensity threshold for grey matter and CSF. I know that Freesurfer scales the intensity so white matter has an intensity of 110 (as can be seen at the bottom of Freeviewer when I open the brianmask.mgz). I was wondering whether there is a threshold value I can use to indicate whether a voxel is part of the CSF with 100% confidence? (2) After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes: recon-long -autorecon2-noaseg -subjid <Subj_ID> I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes? Thank you, Tamara

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Freesurfer 6.0 and MNI template
by Trisanna Sprung-Much 25 Jan '17

25 Jan '17

Me again, Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in MNI305 space or have they been updated to the MNI152 space? many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Freesurfer January 2017