Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Centrum Semiovale Labels in Freesurfer
by Syeda Maryam 27 Oct '15

27 Oct '15

Hello Freesurfer experts, I needed to extract the centrum semiovale from freesurfer labels to use for further analysis. The freesurfer website states that the Centrum semiovale is labeled with 5001 (left) and 5002 (right). I found these labels in the wmparc.mgz volume, however they are labeled as left/right unsegmented white matter. Do these still correspond to the centrum semiovale? Thanks in advance for your help! Maryam

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R: Re: R: import FS-FAST results in FSL
by stdp82＠virgilio.it 27 Oct '15

27 Oct '15

Yes I would like to open with fslview (FSL) the sig.nii.gz of each subject which is computed by seed-based analysis by FS-FAST. I have mask the sig.nii.gz by fslmaths -div I have run: mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg subj/rest/001/register.dof6.dat --hemi rh --o prova.nii.gz but when I open the prova.nii.gz with fslview the windows is empty with a line. Thanks Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 29-set-2015 22.09 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL > >Do you mean surface-based analysis? You'd have to put them back into the >volume using mri_surf2vol, write them out as nifti and then run fslview >on them > >On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >> >> Hi list, >> >> I would like to import FS-FAST results (conjunction maps) in FSL, >> opening them by fslview. >> Could you provide me any suggestion? >> >> Thank you very much >> Best regards, >> >> >> 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. > >

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Re: [Freesurfer] : FOLLOW-UP question: remove label from aseg
by Jacobs H (NP) 26 Oct '15

26 Oct '15

On 10/25/15, 3:29 AM, "Jacobs H (NP)" <h.jacobs(a)maastrichtuniversity.nl> wrote: >Hi. > >Just one another related question: now that I was able to combine left and >right hippocampal subfields with the aparc-aseg correctly, I noticed that >the left and right hippocampal subfields have the same color labels and >codes. What would be the best way to make sure that FreeSurfer understand >that the left and right subfields (e.g. Left and right CA1) are different >areas? > >Thanks! >Heidi > >On 10/21/15, 11:01 PM, "Jacobs H (NP)" <h.jacobs(a)maastrichtuniversity.nl> >wrote: > >>Thanks! Works wonderful! >>Heidi >> >>On 10/21/15, 10:50 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>wrote: >> >>>If you want to remove them, you can use mri_binarize with the --replace >>>option, replacing them with whatever you want. >>> >>>On 10/21/2015 04:38 PM, Jacobs H (NP) wrote: >>>> Hi, >>>> >>>> I am trying to generate a segmentation file containing the aseg+aparc >>>> but replacing the hippocampus with the hippocampal subfields. >>>> With mergeseg I was able to merge the segmentations, but unfortunately >>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in >>>> there (as the area covered by the subfields is not 100% equal to the >>>> hippocampus of the aseg). >>>> How can I remove the remains of the old hippocampal labels? >>>> >>>> Many thanks! >>>> Best >>>> Heidi >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >> >

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Head circumference
by John Anderson 26 Oct '15

26 Oct '15

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Error with Group Analysis using Qdec
by haidong wang 26 Oct '15

26 Oct '15

Hi FS Experts, When I use Qdec for Group Analysis,I come with an error.Here it is. -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl setenv TUTORIAL_DATA /media/work/FC_DATA/ckd-T1 setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR Data table /media/work/FC_DATA/ckd-T1/qdec/qdec.table.dat loaded. Verifying subject data.sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'con_chenchen' in SUBJECTS_DIR Input table: /media/work/FC_DATA/ckd-T1/qdec/qdec.table.dat Subj#, SubjID, Data... 1 con_chenchen con ... I load qdec.table.dat successfully.However,QdecProject couldn't find subject 'con_chenchen' in SUBJECTS_DIR. As a result,when I use FDR for correction,there is nothing showing in the terminal. I did not dowload the tutorial data.what's more,I have not put the subjs in my Freesurfer install path. How can I deal with it? Thanks for your patience and I am looking forward for your prompt reply.

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Issue opening .dmg file for installing freesurfer patch/code addition for brainstem. Error is "image not recognized"
by Jonathan Plasencia 24 Oct '15

24 Oct '15

Hello, I'm trying to segment the brainstem into subparts. I found online for freesurfer 5.3 you can use the following link to install the need codes: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ which was from the following freesurfer question/solution: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42064.html However, when I open the ftp as a guest and try to open the .dmg file I get the error "image not recognized". Looking into why this happens it sounds like the download went bad. I've tried re-downloading the file a few times and am now wondering if the uploaded file was bad? Is there another solution so I can segment the brainstem? Thank you for your help, Jon

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autorecon2 vs autorecon2-cp
by Kasper Jessen 24 Oct '15

24 Oct '15

Dear freesurfer group I have edited my subjects with both control points and brainmask edits. For the re-processing both my CPs and brainmask edits, at the same time i used the following command: - recon-all -base Subject_base -tp Tp1 -tp Tp2 -autorecon2 -autorecon3 -3T Is this a correct way of doing it? I have become in doubt since i have noticed that some use -autorecon2-cp or -autorecon2-pial. However, i have only used -autorecon2-cp if i ONLY have made control points. But since i have done both CPs and brianmask edits i used -autorecon2 -autorecon3. Best regards, Kasper Phd Student -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

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Re: [Freesurfer] Sulcal depth units
by Simon Vandekar 24 Oct '15

24 Oct '15

Hi Bruce, I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. Thanks again, Simon >H I Simon >Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it >Bruce > >> On Oct 22, 2015, at 3:23 PM, Simon Vandekar <simonv(a)mail.med.upenn.edu> wrote: >> >> Hi Bruce, >> >> I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? >> >> >> sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) >>> mean(sulc$sulc) >> [1] -1.236923e-08 >> >>> var(sulc$sulc) >> [1] 0.3276958 >> >>> quantile(sulc$sulc) >> 0% 25% 50% 75% 100% >> -1.72503 -0.42128 -0.03963 0.40072 1.80980 >> >> >> Thanks again, >> Simon >> >> >> >> >> >> Hi Simon >> >> they are originally mm, but I believe we z-score normalize them so that >> the sulc file is 0 mean and unit variance. >> >> cheers >> Bruce >> On Wed, 21 Oct 2015, Simon >> Vandekar wrote: >> >>> Dear Freesurfer experts, >>> >>> >>> I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. >>> Are the units for sulcal depth in mm or are they in arbitrary units? >>> >>> Thanks in advance, >>> Simon

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Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
by Yun Wang 23 Oct '15

23 Oct '15

Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it? > On Jun 25, 2015, at 13:36, Allison Moreau <almoreau(a)nmr.mgh.harvard.edu> wrote: > > Hi Falk and Thomas, > > We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. > > -Allison > > On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: >> Hi Thomas, >> >> this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data. >> >> Best, >> Falk >> >> P.S. Following your instructions one will definitely become a coffee junkie. :D >> >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) >> Gesendet: Mittwoch, 24. Juni 2015 14:35 >> An: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data >> >> Hello! >> >> I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon <https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline <https://github.com/thomastweets/freesurfer-7t-pipeline>. I am happy about any comments! >> >> Best, >> Thomas >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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Re: [Freesurfer] Help with V6
by Douglas Merkitch 23 Oct '15

23 Oct '15

Hello Noah, Could you be more specific as to how you were able to resolve this problem? What additional tweaks were necessary? I too received the same error message: ERROR: Flag -subfields-T1 unrecognized. -all -s 1048_v6beta_hippsubfieldsT1 -subfields-T1 Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 recon-all -s xxxx exited with ERRORS at Fri Oct 23 13:10:17 CDT 2015 I'm running freesurfer-Darwin-OSX-stable-v6-beta-20150921 on a mid 2012 MacPro (OS X 10.8.5). I also installed the Matlab runtime as instructed. Any help would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> Thanks Noah. It doea say on the website that you need the 2012b runtime, but its definitely buried among too much other, less critical stuff Cheers E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com<http://www.jeiglesias.com> www.bcbl.eu<http://www.bcbl.eu> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer<http://www.bcbl.eu/legal-disclaimer> ----- Original Message ----- From: Noah Markowitz <noahb.markow...(a)gmail.com<http://gmail.com>> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Sent: Sat, 04 Jul 2015 13:57:53 +0200 (CEST) Subject: Re: [Freesurfer] Help with V6 Hey Eugenio, I was able to resolve it with the help of another expert. One of the problems definitely was that 2014b doesn’t run on the hippocampal-subfields module. Maybe try adding that as a note to the website as numerous people have access to the 2014b version and 2015a was just released. Thanks again for all the help. Cheers, Noah > On Jul 3, 2015, at 5:12 PM, Eugenio Iglesias <e.igles...(a)bcbl.eu<http://bcbl.eu>> wrote: > > Hi Noah, > this error is pretty weird. Can you please send us the exact command you > executed? > Regarding the runtime: your 2014b runtime won't work. You need to follow the > instructions here: > https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime > Cheers, > Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com<http://www.jeiglesias.com> > www.bcbl.eu<http://www.bcbl.eu> > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer<http://www.bcbl.eu/legal-disclaimer> > > > ----- Original Message ----- > From: "Noah Markowitz" <noahb.markow...(a)gmail.com<http://gmail.com>> > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Sent: Friday, July 3, 2015 4:20:02 AM > Subject: [Freesurfer] Help with V6 > > Hi, > > I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the > error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and > source just as described for previous versions. > > Also, I have Matlab 2014b downloaded on the computer (obviously comes with > runtime) but am unsure if the runtime folder needs to be placed in the FS > folder or is fine where it is. > > Any FS experts help with these two problems and concerns? Much appreciated if > you do. > > Cheers, > > Noah Markowitz > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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