Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

Order of overlays
by Reza Rajimehr 05 Jul '16

05 Jul '16

Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The borders of aparc are always drawn on top of the activity map, which sometimes hide small activation blobs. Is it possible to draw the activity map on top of the aparc borders? Reza

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[TRACULA] ERROR: cannot unpack mosiacs without ASCII header
by Koubiyr, Ismail 05 Jul '16

05 Jul '16

Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail

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Fwd: Failure to use yeo-7/17 networks maps as templates in MRIcron
by Hsiang-Yuan Lin 04 Jul '16

04 Jul '16

Hi Prof. Yeo, I have problems utilizing yeo 7/17 cortical network parcellation maps as templates in MRIcron (I aim to use your cortical parcellation maps to underlay my findings in order to derive the implications based on iFC networks). To be specific, there is an orientation problem in the current version of parcellation maps in MNI space. Thank you for your help in advance. Best, Hsiang-Yuan -- *Hsiang-Yuan Lin, M.D.* *Attending Psychiatrist & Adjunct LecturerDepartment of Psychiatry & Child Mental Health CenterNational Taiwan University Hospital and College of Medicine* email: louislin28(a)gmail.com CV: https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=shari… <https://drive.google.com/file/d/0B3jQGSXih2aeX0tGbXM2d2Rkd0E/view?usp=shari…> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2 -- *Hsiang-Yuan Lin, M.D.* *Attending Psychiatrist & Adjunct LecturerDepartment of Psychiatry & Child Mental Health CenterNational Taiwan University Hospital and College of Medicine* email: louislin28(a)gmail.com CV: https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=shari… <https://drive.google.com/file/d/0B3jQGSXih2aeX0tGbXM2d2Rkd0E/view?usp=shari…> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2

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Re: [Freesurfer] controlling for total gray matter volume (Clara K?hn)
by Arkadiy Maksimovskiy 04 Jul '16

04 Jul '16

Hi Clara, Yes- my apologies. I misunderstood your initial analyses description. Sounds right to me as well. - Arkadiy

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Re: [Freesurfer] longitudinal tracula
by Harms, Michael 04 Jul '16

04 Jul '16

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Question
by Dulce Maria Magdaleno Arroyo 04 Jul '16

04 Jul '16

Hi, I am doing a research about the uterus, in this research I am trying to define the geometry of this organ, so I want to use freesurfer to mapping the uterus into a sphere; as far as I understand I don't need all the brain image processing. I have already a FEM model of the uterus in matlab, and I was wondering if just the command mris_inflate could be used to this task or if I have to consider some other commands? Other question I have is, Do I need to convert my matlab data to .mgh to use the freesurfer commands? If yes, Could you give me some directions to do this task? In advance, thank you so much for your help. Best, DM

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Re: [Freesurfer] controlling for total gray matter volume
by Harms, Michael 04 Jul '16

04 Jul '16

Hi, Why not use total surface area to control for analyses involving area, and mean cortical thickness to control for thickness? I’ve posted to the list before regarding this, so you should be able to find those posts. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms(a)wustl.edu On 7/4/16, 9:12 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Clara Kühn" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of ckuehn(a)cbs.mpg.de> wrote: Do you know, if there are any publications concerning this matter? So far I've found only this http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148852 that controls for tGM only for area and not CT. Cheers Clara ----- Ursprüngliche Mail ----- Von: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> An: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Gesendet: Montag, 4. Juli 2016 15:37:57 Betreff: Re: [Freesurfer] controlling for total gray matter volume sounds right to me Bruce On Mon, 4 Jul 2016, Clara Kühn wrote: > I have decided now to not control for ICV or total gray matter volume >when looking at cortical thickness but to control for total gray matter >volume when looking at surface area. Does that sound about right? > > Cheers, Clara > > ----- Ursprüngliche Mail ----- > Von: "Arkadiy Maksimovskiy" <arkadiym(a)bu.edu> > An: freesurfer(a)nmr.mgh.harvard.edu > Gesendet: Samstag, 2. Juli 2016 18:36:51 > Betreff: Re: [Freesurfer] controlling for total gray matter volume > > Hi Clara, > > If I am understanding your question correctly, you don't need to control >for brain volume when looking at thickness analyses. > > See quote below from this link: > > http://www.freesurfer.net/fswiki/eTIV > > "Note that this correction is only useful in situations where the >structure scales with head size. Outside of this, correction just adds >noise, or provides inaccurate data. In the case of the measures from >Freesurfer, one would apply correction to the volume measures and not >thickness measures. This is because volume scales with head size which is >mostly due to changes in surface area, whereas thickness alone scales to >a much less degree." > > Best, > Arkadiy > > On Sat, Jul 2, 2016 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. controlling for total gray matter volume (Clara K?hn) > 2. cotrolling for total gray matter volume (Clara K?hn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST) > From: Clara K?hn < ckuehn(a)cbs.mpg.de > > Subject: [Freesurfer] controlling for total gray matter volume > To: Freesurfer support list < freesurfer(a)nmr.mgh.harvard.edu > > Message-ID: > < 600644700.119350.1467292783757.JavaMail.zimbra(a)cbs.mpg.de > > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control >for total gray matter volume. Should I use that information from the >CROSS before anything has been registered and smoothed or from the LONG >after they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter >volume when looking at surface area? > > Thanks for your help! > Clara > > > ------------------------------ > > Message: 2 > Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST) > From: Clara K?hn < ckuehn(a)cbs.mpg.de > > Subject: [Freesurfer] cotrolling for total gray matter volume > To: Freesurfer support list < freesurfer(a)nmr.mgh.harvard.edu > > Message-ID: > < 1473114832.117985.1467291666701.JavaMail.zimbra(a)cbs.mpg.de > > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control >for total gray matter volume. Should I use that information from the >CROSS before anything has been registered and smoothed or from the LONG >after they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter >volume when looking at surface area? > > Thanks for your help! > Clara > > _______________________________________________ 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 materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] controlling for total gray matter volume
by Arkadiy Maksimovskiy 04 Jul '16

04 Jul '16

Hi Clara, If I am understanding your question correctly, you don't need to control for brain volume when looking at thickness analyses. See quote below from this link: http://www.freesurfer.net/fswiki/eTIV "Note that this correction is only useful in situations where the structure scales with head size. Outside of this, correction just adds noise, or provides inaccurate data. In the case of the measures from Freesurfer, one would apply correction to the volume measures and not thickness measures. This is because volume scales with head size which is mostly due to changes in surface area, whereas thickness alone scales to a much less degree." Best, Arkadiy On Sat, Jul 2, 2016 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. controlling for total gray matter volume (Clara K?hn) > 2. cotrolling for total gray matter volume (Clara K?hn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST) > From: Clara K?hn <ckuehn(a)cbs.mpg.de> > Subject: [Freesurfer] controlling for total gray matter volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <600644700.119350.1467292783757.JavaMail.zimbra(a)cbs.mpg.de> > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control > for total gray matter volume. Should I use that information from the CROSS > before anything has been registered and smoothed or from the LONG after > they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter > volume when looking at surface area? > > Thanks for your help! > Clara > > > ------------------------------ > > Message: 2 > Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST) > From: Clara K?hn <ckuehn(a)cbs.mpg.de> > Subject: [Freesurfer] cotrolling for total gray matter volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <1473114832.117985.1467291666701.JavaMail.zimbra(a)cbs.mpg.de> > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control > for total gray matter volume. Should I use that information from the CROSS > before anything has been registered and smoothed or from the LONG after > they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter > volume when looking at surface area? > > Thanks for your help! > Clara > > -- > Clara K?hn, 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 > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 149, Issue 6 > ****************************************** > > > 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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Tissue probability maps from aseg.mgz
by Lee Subin Kristine 04 Jul '16

04 Jul '16

Dear FreeSurfers, Is it possible to get tissue probability maps (for the purpose of using them in spm DARTEL, PVElab, etc) out of aseg.mgz? I did read in a previous post (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006384.h…) that you can use mri_ca_label with the option -write_probs, but I could not find a -write_probs option. If not, I'm wondering is there is any other possible way to get tissue probability maps from FreeSurfer? Any help would be much appreciated. Regards, Subin

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trac-all error (bvecs and bvals don't have same number of entries)
by Lars M. Rimol 04 Jul '16

04 Jul '16

Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 ---------- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. ------------------------------------------------------------------- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Freesurfer July 2016