Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

Volume to Surface mapping looks great for Vols created in FSL but not SPM
by Rita Elena Loiotile 15 Feb '18

15 Feb '18

Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command. I can attach pictures of the comparison if you'd like. Thanks in advance, Rita

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Nonlinear CVS registration into average brain for coordinates
by Zhou, David Wei 10 Jan '18

10 Jan '18

Hi all, I have a data set of 14 subjects with intracranial (both cortical and subcortical) electrode implants, already recon'ed in Freesurfer, with an average brain + surface computed of these subjects. I would like to map each subject's electrode coordinates (a set of RAS points) into the average brain using a nonlinear transformation to account for individual deviations in surface topology. I'm trying to figure out the steps that must be taken to achieve this. With my average brain as a template, it seems like I would use mri_cvs_register to produce each subject warped onto the template. After generating those warps, how does one apply the same warp to a set of coordinates, for example to find out where my electrodes end up in the template brain? Which output file in .../cvs contains the data necessary to compute the coordinates in the template? I'd appreciate any instruction, thanks! David

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How to output particular area from stats subdir
by Jing Gu 09 Jan '18

09 Jan '18

Dear FreeSurfer Developers, By using the following code, we can get volume data of different areas from stats file. asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt How can I get information of one or two areas, such as hippocampal? thanks Best, Gina

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Dec '17

20 Dec '17

Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>> Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thank you for your help. > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the > system language everything was genereted correctly and trac-all -prep ran without any errors. > I'm so glad. > > Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was reading > about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? > > Sincerely, > Florian > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> > > Hi Florian - Can you please change the decimal commas to points and try > again? > > a.y > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Here are the bvec and bval files you asked me about. > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> > > > > Hi Florian - Can you please also attach the bvecs/bvals files from the > > dmri directory? > > > > Thanks, > > a.y > > > > On Sun, 18 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia, > > > > > > Thanks for your help. I renamed the directories and reran trac-all. It > > > worked for the moment. > > > However, then I got another error: "bvecs and bvals don't have the same > > > number of entries." > > > I don't know why, because they actually have the same number of entries. > > > > > > I attached the logfile so that you may see what is going on. The error > > > occours at line 1463. > > > > > > Thank you in advance for your help. > > > > > > Sincerely, > > > Florian > > > > > > > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > > > > > Hi Florian - I see what's going on. Can you please rename the directory > > > /data/physics/florian/nii into something that doesn't include "nii", and > > > rerun? Because "nii" is a file extension, this confuses some of the > > > scripts. > > > > > > Thanks, > > > a.y > > > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > > > > > Hi Anastasia > > > > > > > > I ran the command you sent me and it runs without any errors. > > > > I also attached the command line for you. > > > > > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > > > same kind of problems. > > > > > > > > sincerely > > > > Florian > > > > > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > > > >>> > > > > > > > > Hi Florian - Can you please run this command directly on the command line > > > > and see if there are any errors? > > > > > > > > flip4fsl > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > > > > > Thanks, > > > > a.y > > > > > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > > > > > Hi Anastasia > > > > > > > > > > Thank you for your answer. > > > > > > > > > > Yes, those files exist. > > > > > I also extracted the bvec an bval files with anotther software then > > > > dcm2nii > > > > > and i keep getting the same kind of error. > > > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > > > testdata for running tracula. > > > > > > > > > > sincerely > > > > > Florian > > > > > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > > > >>> > > > > > > > > > > Hi Florian - Do these files exist? > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > > > s > > > > > > > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > > > s > > > > > > > > > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > > > this > > > > > has nothing to do with the error you're getting) I have to warn you that > > > > > you may not be able to get good results running probabilistic > > > tractography > > > > > on this data. It looks like you're acquiring the same 6 diffusion > > > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > > > reconstructing the tensor model, but will probably not be sufficient for > > > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > > > tracula). Your scan time is better spent acquiring 48 different > > > > > directions, rather than the same 6 directions 8 times. > > > > > > > > > > a.y > > > > > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I have been trying to run tracula on my data and i keep getting the > > > same > > > > > > kind of error repeatedly. > > > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > > > diffusion protocol. However, tracula cannot read the bvec and bval > > > data > > > > > out > > > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > > > the > > > > > > config file. > > > > > > After doing so, I got the error which says that tracula cannot find > > > the > > > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > > > I have tried many options, but still cannot find a solution. > > > > > > I am hoping to get some troubleshooting help. > > > > > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > > > files. > > > > > > To uphold patient confidentiality, I have encode the name patient's > > > data > > > > > as > > > > > > "AAAAAA". > > > > > > > > > > > > I believe the problems are the bvec and bval files or their > > > structures. > > > > > The > > > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > > > 268 > > > > > and > > > > > > 1480 - 1484. > > > > > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > > > > > With kind regards, > > > > > > > > > > > > Florian Borsodi > > > > > > Department of Neurology > > > > > > Medical University of Graz > > > > > > > > > > > > > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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A note about the Freesurfer license file
by Z K 14 Dec '17

14 Dec '17

Hello All, Users on newer linux distributions who upgrade from Freesurfer version 5.3 to version 6.0 may get the following error message: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- This is a known issue, and as the message says, it is resolved by downloading a newly formatted license file from our registration page: http://surfer.nmr.mgh.harvard.edu/registration.html Simply overwrite the old license file with the newly formatted one. Sorry for any inconvenience this may have caused. -The Freesurfer team

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mri_cvs_register: how to read/import .m3z warp file
by Stefano Zappalà 06 Nov '17

06 Nov '17

Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to the MNI space. I was wondering how file format .m3z is organized, in order to read it with, for example, matlab. Or if there are simpler file format to convert the warp field to. No information about it seems to be reported in the website. Moreover, I've searched the list and a similar question was not answered. I was wondering if you have some suggestions in reading the output warp field of mri_cvs_register. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04 LTS Many thanks, Stefano.

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preproc-sess
by Jiahe Zhang 09 Oct '17

09 Oct '17

Dear Freesurfer experts, I have two questions regarding preproc-sess: 1) What is the default algorithm that does the functional-anatomical registration? And is there any way to change the default to other types of registration methods? 2) If I do not want to normalize to template, i.e. I want to keep the image in native space, should I be using -noreg or -noinorm? Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789

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TMI(total motion index) of diffusion MRI
by 이 정환 06 Oct '17

06 Oct '17

Hello I’m attempting to analysis diffusion MRI using TRACULA. As mentioned on article "Spurious group differences due to head motion in a diffusion MRI study", I tried to calculate TMI(total motion index) first. The problem is that, upper and lower quartile of Percent Bad Slices are both 0. Upper and lower quartile of avg dropout score are both 1. Calculating TMI on some subjects using those values figured out at questionable results because difference of upper and lower quartile values is used as denominator in formula. I those cases, should I exclude Percent Bad slices and avg dropout score calculating TMI? Does anyone have any thoughts on it? Thanks in advance.

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dev -FLAIRpial bug?
by Hibert, Matthew Louis 28 Sep '17

28 Sep '17

Hi FS Devs, We're running some reconstructions of 7T MPRAGEs with the -FLAIRpial flag turned on using the Martinos install of the dev version. Recently we encountered the error in the attached recon-all log in which it appears that recon-all is trying to use the aseg.mgz before it has been created. According to the dev table online, the mris_make_surfaces command as part of the -FLAIRpial processing should use aseg.presurf.mgz, but it crashes with an error that it was unable to open aseg.mgz. Thanks, Matt

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patch for ribbon mgz failure
by Maria Gloria Rossetti 08 Sep '17

08 Sep '17

Hi freesurfer team, I got the same error described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45983.html and, as suggested, I tried to copy in $FREESURFER_HOME/bin/ the patch from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats but I cannot find the URL. I also found some patches here : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ but I don't know which one I'm supposed to use. Any advice? Thanks! Gloria

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Freesurfer August 2017