Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

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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Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

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mri_cvs_register failure from missing shared lib
by Michael Waskom 25 Apr '17

25 Apr '17

Hi, I had mri_cvs_register die on me when it couldn't find a shared library. Relevant bit is (full log is attached): mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory Freesurfer bugr info: -------------------- FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 ---------------------- Any thoughts on how to proceed? Thanks! Michael

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FSFAST mkcontrast-sess with spmhrf 2 question
by Joseph Dien 25 Mar '16

25 Mar '16

Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

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some questions about optseq
by charujing123 15 Jan '16

15 Jan '16

Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123

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DEPRECATED warning in Freesurfers
by Peter Wendorff 13 Oct '15

13 Oct '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I'm working with freesurfer as a software developer in a cloud project. My task is to enable control of freesurfer via network (e.g. REST interfaces). That works fine so far, but I stumbled over the following pearl deprecated warning: "Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer//mni/bin/sharpen_volume line 153." Which has been printed to the log files repeatingly. I'm not a pearl expert, but I think, it's due to a more up to date pearl version used here, that deprecated the usage of ? delimiters for patterns without explicit operator. Using / as a delimiter works fine. I changed that locally to (new line 153): ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; (the original code here was): ($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; I'm not sure this is the best solution. It's even not strictly necessary to change this - it's only a warning that's thrown; but I think, it's useful. How can I submit this as a patch? Is it enough to report here? What to do? regards Peter Wendorff P.S.: For referene the header parameters of my sharpen_volume for revision comparison: #---------------------------------------------------------------------------- #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author: bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header - ---------------------------------- #@NAME : sharpen_volume #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: modifies intensities so as to produce a sharper histogram #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : February 28, 1996 #@MODIFIED : #----------------------------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlGTa5kACgkQi8ffXNvWmYSCUQCghMg1EffqfeJK4PSfo20uF8/J H0MAnjJc0WbHPf5gLDUw70K8fnQPjS+L =g+6e -----END PGP SIGNATURE-----

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PhD position in tractography validation, Inserm U930 "Brain and imaging" lab, University François-Rabelais of Tours
by Frédéric Andersson 06 Oct '14

06 Oct '14

"A funded PhD Student position will be available in the “Brain and Imaging” Inserm unit (national institute for health) settled in Tours, France, from October 1st, 2014 to September 30th, 2017. During this time period, the candidate will have: (1) to develop tools and pertinent criteria for comparison of MR-based tractography results to data obtained from dissection; (2) to compare different algorithms used for MR-based tractography; (3) to develop a tool aiming to help decision making for the choice of optimal algorithms and parameters used for tractography. This work will be co-directed by Pr C Destrieux (Anatomist) and Pr G Venturini (Computer Science) in the university of Tours. It will be funded for the whole time period by a grant we obtained from the Ministry of Research (about 1400 € per month). Potential candidates have to send a letter and a CV to christophe.destrieux(a)univ-tours.fr and gilles.venturini(a)univ-tours.fr before the 15th of April. After an internal selection of the applications, they will have to defend their candidateship during an interview organized by the Doctoral School of the university at the end of May 2014."

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bbregister for MRA
by SHAHIN NASR 30 Sep '14

30 Sep '14

Hi Surfers I want to use bbregister to register my MRA scans to the structural scans. The first attempts by using these parameters came out OK but not perfect: bbregister --s <Subject_ID> --mov MRA.nii --init-fsl --reg register.dat --bold However, there are obvious problems around frontal areas. I have to admit that one of the reasons for this imperfect registration may be that MRA scans do not cover the whole brain. However, they still cover a large portion of it. I was wondering if there is any argument in bbregister command that may help me improve the quality. It is very fine if it increases the registration time. Regards P.S.: using --t2 in bbregister (instead of --bold) generated the same outcome but --t1 was completely off. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
by Douglas Greve 25 Sep '14

25 Sep '14

Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: > Dear Dr. Greve, > > Is it possible to register a nonstructural MR sequences (e.g. an ADC > map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, > using the segmentation from the aseg (or aparc+aseg) file to output a > mean ADC value for each anatomic area segmented? > > Thank you for your time and consideration. > > Best wishes, > > Sal > > Salil Soman, MD, MS

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FsFast Functional Connectivity Analysis
by Jiahe Zhang 12 Sep '14

12 Sep '14

Hi Doug, I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth…) I was able to successfully run the following commands (nothing errored as far as I can tell) but the resulting partial correlation and significance maps turned out to be empty. Could you take a look at the commands and let me know if anything can be improved? 1. PREPROC preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh -mni305-2mm -fsd bold -per-run -stc up 2. SEED CONFIG fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config 3. SEED TIMECOURSE fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config (wm.dat and vcsf.dat were similarly created) 4. ANALYSIS CONFIG mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 5 -per-run -lpf .1 5. ANALYSIS selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001 Thanks, Jiahe -- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789

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Freesurfer August 2014