Freesurfer

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30076 discussions

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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Slim down FS6
by Marmaduke Woodman 05 Feb '17

05 Feb '17

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

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Specification of computer
by Aziz Nanthaamornphong 04 Feb '17

04 Feb '17

Hi experts, I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data. Please let me know what the best spec of the computer that can reduce the time to 2-3 hours (if possible). Thank you, Aziz

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CUDA in FS6?
by Chris Adamson 03 Feb '17

03 Feb '17

Freesurfer devs, Are the CUDA binaries still being developed in FS6? Are they compatible with the CPU only versions? I remember asking questions about this a while ago and apparently the cuda binaries were no longer being developed in favour of openmp. Thanks in advance, Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chris.adamson(a)mcri.edu.au T 03 9936 6780 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Surface based analysis for hippocampus subfield thickness
by Dev vasu 03 Feb '17

03 Feb '17

Dear all, Is there any approach that you recommend to quantify that changes in cortical thickness in hippo campus sub fields , how could i perform Surface based cortical thickness changes using freesurfer. Thanks Vasudev

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license file not working
by Anthony Dick 03 Feb '17

03 Feb '17

Hello, I have been using Freesurfer for a number of years, and just installed v6.0. I run into this problem: -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I have a valid .license file, in the Freesurfer home directory Last login: Thu Feb 2 15:04:01 on ttys005 -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni [38c9862eb0b0:~] adick% cd /Applications/freesurfer [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license -rw-r--r-- 1 root wheel 140 Feb 2 15:06 .license [38c9862eb0b0:/Applications/freesurfer] adick% Any ideas? Thanks! Anthony -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org

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Kind Request - Trouble with FreeSurfer LICENSE file
by Abhinav Kurada 03 Feb '17

03 Feb '17

To Whom It May Concern: I am currently unable to successfuly register my copy of FreeSurfer with the license keys I received. Although I found a LICENSE file in the FreeSurfer program directory after successfully installing the program, I could not find the CUT Here lines as well as the location of placing the text emailed to me. Could you please assist me in helping register my copy of FreeSurfer? Thank you in advance. Sincerely, Abhinav Kurada Columbia University

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Re: [Freesurfer] Multiple comparison question
by neuroimage analyst 03 Feb '17

03 Feb '17

Thanks, Anderson. If there are several other measures such as volume, thickness, FA, can I then put them in a single csv file and run the command or I have to create 3 csv files, one each for volume, thickness,and FA and also invoke -corrmod? Thanks Regards VM On Feb 2, 2017 1:01 AM, "Anderson M. Winkler" <winkler(a)fmrib.ox.ac.uk> wrote: Hi VM, Please see below: On 1 February 2017 at 02:38, neuroimage analyst < neuroimage.analyst(a)gmail.com> wrote: > Hi, > > We extracted volume measures from 7 ROIs in 2 groups and compared > a) Mean of each ROI volume between group, and compared independently such > as > i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2 > ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2 > and so on > This means 7 comparisons, or 14 if you test both directions (tails) separately. > > b) Plotted the mean ROI volume for 2 independent measures and compared > whether the slope between and within group is significantly different. such > as > i) Slope of ROI1 is positively associated with MoCA , age (grp1) ? > ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ? > iii) Slope of ROI1 vs MoCA (grp1) is significantly different than slope of > ROI1 vs MoCA (grp2) ? > iv) Slope of ROI1 vs MoCA (grp2) is significantly different than slope of > ROI2 vs MoCA (grp2) ? > These sound tests for main effects and interaction, with various combinations possible. > > Q1) Do we have to perform multiple comparisons for (a) and (b)? > Yes. > Q2) If yes, do we correct across 7 measurements for (a) and 2 measurements > for (b) or 7 measurements for both (a) and (b)? > You could put the values for the 7 ROIs in a table in .csv format, with one column per ROI and one row per subject. This would be the input data. Create a design matrix as: EV1: 0 or 1 coding for group 1 EV2: 0 or 1 coding for group 2 EV3: MoCA group 1 EV4: MoCA group 2 EV5: Age group 1 EV6: Age group 2 etc Then define a set of contrasts such as: C1: [1 -1 0 0 0 0 ...] - This tests if mean for group 1 > mean for group 2 C2: [-1 1 0 0 0 0 ...] - This tests if mean for group 1 < mean for group 2 C3: [0 0 1 -1 0 0 ...] - This tests if the slope for MoCA for group 1 > slope for MoCA for group 2 C4: [0 0 -1 1 0 0 ...] - This tests if the slope for MoCA for group 1 < slope for MoCA for group 2 C5: [0 0 1 0 0 0 ...] - This tests if slope for MoCA for group 1 > 0 C6: [0 0 -1 0 0 0 ...] - This tests if slope for MoCA for group 1 < 0 etc You'd run this analysis in PALM with something as: *palm -i input.csv -d design.mat -t design.con -corrcon -o myresults -logp* Hope this helps! All the best, Anderson > There is evidence to both performing and nonperforming multiple > comparisons In the literature. > > Any response (hopefully pointing to a literature) will be greatly > appreciated. > > Thanks > > Regards > > --VM > > _______________________________________________ > 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 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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how to export cortical thickness in to .txt
by shi yao wang 03 Feb '17

03 Feb '17

Dear Fs experts: I would like to use mris_anatomical_stats to calculate 35 cortical regions thickness. I am using following command: mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh

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Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}
by Joe Necus (PGR) 03 Feb '17

03 Feb '17

Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag. Joe ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: 02 February 2017 22:56 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) Hi Joe there are slight differences, and for sure we reserve the right to use the knowledge that it is a FLAIR scan in the algorithms, so you should probably rerun cheers Bruce On Thu, 2 Feb 2017, Joe Necus (PGR) wrote: > > Hello, > > > I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether > there is any difference between using the -T2 -T2Pial and -Flair flags. > > > I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and > would like to know whether I need to go back and instead re-run with the -FLAIR flag instead. > > > Thanks a lot, > > Joe > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<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 ... 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 mycompliancereport.com<http://www.partners.org/complianceline> www.partners.org ComplianceLine engages in the business of providing 24-hour toll-free hotlines for the reporting and tracking of compliance concerns to assist in the identification of possible unethical, illegal or questionable behavior. but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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