Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

[FSFAST] Matlab parallel
by Seung-Goo KIM 06 Feb '17

06 Feb '17

Hi all, So this is a question about running FAST through matlab parallel desktop: I know it is very funny (and inefficient) because I open up a bash in the matlab to run a csh script that generates and runs a matlab code, but just I’m familiar with matlab in doing many things including string manipulation, so that’s how I’m doing now. If there are matlab scripts that does a similar thing as csh scripts, it would be nice. Anyway, I realized that I cannot run all the fitting with different parameters and with the identical name of model (the GLM directory name) at the same time because the code appears to refer to the directory at $SUBJECTS_DIR. But I tried to run multiple subjects (with all different GLM names in their own native spaces) through MATLAB on a server, it returns (seems just one of random subject): > ERROR: could not read /tmp/tmp354512.nii > rm: cannot remove ‘/tmp/tmp354512.nii’: No such file or directory > ERROR: loading ${filename}.nii.gz as analyze So I traced back to the functions that return those errors (i.e., load_nifti.m run in MRIread.m) and it seems to be something with the temporary directory managed by matlab workers. The temporary file seems to be only necessary for nii.gz file. If so, I would rather just use .nii file format (or maybe .mgz?) format instead of dealing with the void complexity. Then can it be done by just putting: > setenv(‘FSF_OUTPUTFORMAT’,’.mgz’) before I run "preproc-sess" and "selxavg3-sess” in my scripts? Best regards, -- Seung-Goo KIM

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possible atlas error to report
by Levman, Jacob 06 Feb '17

06 Feb '17

Hi there, I've been conducting an asymmetry analysis based on FreeSurfer measurements. There are regions of the brain with known left-right asymmetry such as BA44 which exhibits strong leftward asymmetry (the left side is bigger than the right). This is accurately reflected when you compare the BA44 GrayVol measurement from lh.BA.thresh to rh.BA.thresh. However, in the lh.BA and rh.BA results, the BA44 GrayVol measurements consistently indicate a rightward asymmetry (right side larger than the left side) though this conflicts with known findings in the literature for this region of the brain and is the opposite pattern to that produced in lh.BA.thresh and rh.BA.thresh. This indicates that the lh.BA and rh.BA results may be left-right inverted in BA44 and possibly in other regions as well. Thanks, Jacob ?

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extract values uncorrected clusters
by Clara Kühn 06 Feb '17

06 Feb '17

Dear FreeSurfer experts, I did a group analysis in QDEC for the symmetric percent change from pre to post and have a couple of clusters that don't survive the Monte Carlo correction. I want to extract the values for each time point per subject for those clusters that are bigger than 150 vertices to look at individual trends. How could I achieve this? Thank you for your help. Clara ----- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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R: Re: Hipposubfields in FreeSuerferColorLUT.txt
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Thanks Eugenio for your response. My apologies but this matter is unclear to me.If I would use results for FS-FAST how I can identify for example CA1 right from CA1 left?Additionally, for enthorinal which is the correct code in FAST?Stefano ----Messaggio originale---- Da: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Data: 6-feb-2017 15.54 A: "stdp82(a)virgilio.it"<stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Hipposubfields in FreeSuerferColorLUT.txt Ciao Stefano, The results for the left and right hippocampi are in different files, so there’s no ambiguity despite the fact that they indeed share the same label codes. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Feb 2017, at 13:18, stdp82(a)virgilio.it wrote: Hi list, within FreeSuerferColorLUT.txt, do the numbers between 200-226 descrived the hippo-subfield outputs? Additionally, how can I obtain separate right and left masks? Thanks Stefano _______________________________________________ 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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Cortical thickness changes in Hippocampus sub fields
by Dev vasu 06 Feb '17

06 Feb '17

Dear all, I would like to perform Group ROI analysis between healthy controls and BVF patients where i would like measure cortical thickness changes between healthy controls and BVF, what changes should i adopt to my initial preprocessing tasks using recon-all in order to evaluate changes in cortical thickness and possibly sulcal depth. Any suggestions are greatly appreciated . Thanks VAsudev

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Hipposubfields in FreeSuerferColorLUT.txt
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Hi list,within FreeSuerferColorLUT.txt, do the numbers between 200-226 descrived the hippo-subfield outputs?Additionally, how can I obtain separate right and left masks? Thanks Stefano

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using -bigventricles flag in FS 5.3
by Mehul Sampat 06 Feb '17

06 Feb '17

Hi Folks, I have a question about the usage of the -bigventricles flag in FS 5.3. 1. Suppose i run recon-all with -bigventricles option. 2. Then i add control points and run recon-all with the -autorecon2-cp as described in the recon-all help. USAGE: recon-all 3. The recon-all help mentions "-autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg" My question is: when i run recon-all the second time with the -autorecon2-cp flag, do i need to include the -bigventricles option again ? In general, if the first round of processing used -bigventricles, should it be always used if recon-all is re-run after making edits ? Thanks Mehul ps: can you believe the Patriots won SB51 !! :-)

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Special Issue, JAD
by Juan Manuel Górriz Sáez 06 Feb '17

06 Feb '17

Dear Colleagues, In collaboration with the Journal of Alzheimer’s Disease, we are organizing a supplementary issue entitled "Multivariate Approaches in Neuroimaging: Assessing the Connectome of Alzheimer's Disease", hosted by Juan Manuel Górriz, Juan Eugenio Iglesias and Javier Ramírez. As host editor, I would like to encourage you to contribute to this topic. Please find more information about Research Topics below, including the publishing fees that apply. You can also visit the homepage we have created on the JAD website, which defines the focus of the topic, and where all published articles will appear. http://www.j-alz.com/contents http://www.j-alz.com/fees With your agreement to take part, I would request you to submit an abstract in advance of any manuscript submission. All contributors should format their articles per our instructions to authors (http://www.j-alz.com/prep/) and submit the manuscripts to our online submission site (http://mstracker.com/submit1.php?jc=jad) Authors should specify in their cover letter that is for the supplementary issue and mention the lead editor´s name. Let me know if you have any questions about my research topic. I look forward to hearing from you soon. Please note the submission deadline for this supplementary issue: Apr 30, 2017 With best regards, Prof. JM Gorriz Guest Associate Editor Dr.Dr. Juan Manuel Górriz Sáez Catedrático de Universidad Dpto. Teoría de la Señal, Telemática y Comunicaciones Facultad de Ciencias, Universidad de Granada Avda. Fuentenueva s/n CP 18071 https://www.researchgate.net/profile/Juan_Gorriz http://www.ugr.es/~gorriz/ -------- CLUSULA DE CONFIDENCIALIDAD: "This message is intended exclusively for its addressee and may contain information that is CONFIDENTIAL and protected by professional privilege. If you are not the intended recipient you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited by law. If this message has been received in error, please immediately notify us via e-mail and delete it".

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QATools FreeView
by Melanie Ganz 06 Feb '17

06 Feb '17

Hi, back in the day Louis mentioned that he was preparing a script for using the QAtools in Freeview. (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36765.html) Is there a script like that available by now? It's not yet on http://surfer.nmr.mgh.harvard.edu/fswiki/QATools#FutureDirections. Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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Re: [Freesurfer] Slim down FS6 (Marmaduke Woodman)
by Alex Cohen 05 Feb '17

05 Feb '17

Have you looked at the modifications for the BIDS App version: https://github.com/BIDS-Apps/freesurfer I believe the latest image (using FS6) is only 6.37GB and you could bypass the run.py script with --entrypoint bash to run your typical recon-all commands -Alex ---------------------------------------------------------------- Alexander Li Cohen, M.D., Ph.D. E-mail: Alexander.Cohen2(a)childrens.harvard.edu (Medical/Science Email) E-mail: alexcohen(a)gmail.com (Lifetime Email) ---------------------------------------------------------------- On Sun, Feb 5, 2017 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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 > 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. Problem with using tksurfer to take snap shot with .tcl (Hao wen) > 2. Slim down FS6 (Marmaduke Woodman) > > > ---------- Forwarded message ---------- > From: Hao wen <hao.freesurfer(a)hotmail.com> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Sun, 5 Feb 2017 09:28:19 +0000 > Subject: [Freesurfer] Problem with using tksurfer to take snap shot with > .tcl > > Hello: FS experts: > > I am now integrating to use tksurfer to take snapshot from command line > automatically, and my command is like this: > > ``` > > cmd = "tksurfer %s %s inflated -tcl %s" % (subject, hemi, os.path.join(os.path.dirname(sys.argv[0]), "snap_tksurfer.tcl")) > > ``` > > so i use -tcl to define the behavior of tksurfer, but I go t a bug inside > the tickle script, > > > ##curv > puts "shitaaaaa" > puts stdout [pwd] > puts stdout $env(SUBJECT_NAME) > puts [trace vinfo lablpth] > read_binary_curv > puts "shittttttttt!!!, has bug here" > > I debug it and found that it can not really run this command: > read_binary_curv, before, it can take some snapshots and save it to be rgb > format, and i will also give you the output from the terminal: > > > *Successfully parsed tksurfer.tcl* > *shitaaaaa* > > */Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional* > *sub-PREVDEMALS0010001BE_ses-M0* > > *subject is sub-PREVDEMALS0010001BE_ses-M0* > *hemi is lh* > *surface is inflated* > *surfer: current subjects dir: > /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional* > *surfer: not in "scripts" dir ==> using cwd for session root* > *surfer: session root data dir ($session) set to:* > *surfer: > /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional* > *checking for nofix files in 'inflated'* > *Reading image info > (/Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0)* > *Reading > /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0/mri/orig.mgz* > *surfer: Reading header info from > /Users/junhao.wen/Hao/Dataset/test-data/recon-alled-result-1sub/analysis-series-default/subjects/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0/mri/orig.mgz* > *surfer: vertices=98465, faces=196926* > *surfer: single buffered window* > *surfer: tkoInitWindow(sub-PREVDEMALS0010001BE_ses-M0)* > *setting percentile thresholds (-1.00, 0.00, 0.00)* > *surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl* > *tksurfer: run tcl script: > /Users/junhao.wen/Hao/Project/clinica_realted/CAPS_qa_clinica/snap_tksurfer.tcl* > *Reading /Applications/freesurfer/tktools/tkm_common.tcl* > *Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl* > *Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl* > *Reading /Applications/freesurfer/tktools/tkUtils.tcl* > *Successfully parsed tksurfer.tcl* > *reading white matter vertex locations...* > > I will also attach you the tcl file, any suggestion will be appreciated:) > > PS: I know that FS right now recommand us to use freeview, do you have the > similar behavior like using tcl file to define the behavior of freeview to > take the snapshots??? > > Good day > Hao > > > > ---------- Forwarded message ---------- > From: Marmaduke Woodman <mmwoodman(a)gmail.com> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Sun, 5 Feb 2017 14:23:25 +0100 > Subject: [Freesurfer] Slim down FS6 > Hi > > I'm using just the standard structural recon-all pipeline, nothing else. > FS6's directory totals just over 9 GiB. Is there a way to slim that down, > or is it all required for the structural pipeline? > > I'm using Docker containers, hence trying to slim down the image size. > > Thanks, > Marmaduke > > > > > > _______________________________________________ > 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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Freesurfer February 2017