Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Re: [Freesurfer] 3_group_comparison
by Lee Tirrell 15 Mar '16

15 Mar '16

Hi Dusan, setenv is used when you are using tcsh. since you are using bash, you can run this command to set your language: export LANG=en_US.UTF-8 Hope this helps. Best, Lee On Tue, 29 Sep 2015, Dusan Hirjak wrote: > Thank you very much for your suggestion. Now it has worked well. > However, I am having trouble running the simulation via: > > mri_glmfit-sim --glmdir NSS_3_GR.glmdir --cache 4 abs --cwp 0.05 --2spaces > > ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > > > Where can I set up the EN language with "setenv LANG en_US.UTF-8"? > > > I am getting this message: > > > bash-3.2$ setenv LANG en_US.UTF-8 > > bash: setenv: command not found > > > How can I change the language? > > > Many thanks! > > Dusan > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: rpwang(a)nmr.mgh.harvard.edu > Date: Mon, 28 Sep 2015 19:35:12 -0400 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 3_group_comparison > > Was the path of the overlay file correct? It looks like it can’t find the file. Try providing the full path of the overlay file in the freeview command. > > Best, > Ruopeng > > On Sep 28, 2015, at 6:46 PM, Dusan Hirjak <dusanhirjak(a)hotmail.com> wrote: > > Many thanks!!!, yes, freeview has opened, but I am still not seeing any results, just the "lh.inflated" > It says: "Failed to load surface overlay" > > and than I got the following message: > > bash-3.2$ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d > 2015-09-29 00:41:53.887 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.889 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.905 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.906 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.921 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.922 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > Did not find any volume geometry information in the surface > ø;C 8Íÿ¿ø;C È+’Àá > > reading colortable from annotation file... > colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > could not read overlay data from /users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > 2015-09-29 00:42:02.445 Freeview[22049:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: > > I dont understand the problem. Do you have any ideas??? > > Thank you! > > Dusan > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > From: greve(a)nmr.mgh.harvard.edu > > Date: Mon, 28 Sep 2015 18:33:50 -0400 > > Subject: Re: [Freesurfer] 3_group_comparison > > > > I think it needs a -f before the surface > > > > On 09/28/2015 06:27 PM, Dusan Hirjak wrote: > > > Many thanks, yes, it did work well. > > > > > > But, than I ran "freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d" > > > > > > and got the following message: > > > > > > bash-3.2$ freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d > > > > > > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable > > > > > > Unrecognized sub-option flag 'annot=aparc.annot'. > > > > > > > > > Freeview has opened, but it showed no results at all:-( > > > > > > > > > What should I do? I read that one has to upgrade the newest > > > freeview-version? Is it possible to get the newest version without > > > installing freesurfer again? > > > > > > Many thanks! > > > > > > Dusan > > > > > > > > > ------------------------------------------------------------------------ > > > Date: Mon, 28 Sep 2015 11:35:50 -0400 > > > From: greve(a)nmr.mgh.harvard.edu > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] 3_group_comparison > > > > > > Did you include the back slashes in your command? If so, remove them > > > and retry. > > > > > > On 9/25/15 7:11 PM, Dusan Hirjak wrote: > > > > > > Dear Freesurfer experts, > > > > > > I am trying to compare 3 groups (aut, sch, ges) according to > > > thickness, area and LGI at once (omnibus test). > > > > > > I did run the following command: > > > > > > mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in > > > thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out > > > lh.NSS_3_GR.thickness.15.mgh > > > > > > > > > This step did work properly:-) > > > > > > > > > > > > Now, Im trying to run the following command, but it does not work: > > > > > > > > > mri_glmfit \ --y lh.NSS_3_GR.thickness.15.mgh \ --fsgd > > > NSS_3_GR.fsgd dods\ --C contrasts.mtx \ --surf fsaverage lh \ > > > --cortex \ --glmdir NSS_3_GR.glmdir > > > > > > > > > I got this message: "ERROR: Option--y unknown" > > > > > > > > > What am I doing wrong? > > > > > > > > > Thank you for your help! > > > > > > > > > > > > Best regards > > > > > > > > > Dusan > > > > > > > > > _______________________________________________ > > > 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 > > > 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 > > > > -- > > 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 > _______________________________________________ > 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 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] Sulcal depth units (Simon Vandekar)
by Simon Vandekar 22 Jan '16

22 Jan '16

Hi Bruce, The units are not standardized because the standard deviation across the surface does not equal 1. >From line 227 in mris_inflate.c it says that the sulc file is demeaned before it is written out: MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */ However I am still unclear on what the units are. They are too small to be millimeters. Given other published measurements of sulcal depth I think they might be in centimeters, but can you confirm? Thanks again, Simon >Hi Simon > >I just took a look at the code and I believe that we make it 0 median >(not mean) and unit standard deviation. The curvatures can get quite large >in regions where the vertex spacing is small and the median is robust to >this. > >cheers >Bruce > > >On Sat, 24 Oct 2015, Simon Vandekar wrote: > >> 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

3 2

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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how to display individual Desikan parcels?
by Mihaela Stefan 05 Jan '16

05 Jan '16

Hello Freesurfers, I would like to be able to display just a few parcels from the Desikan atlas on the fsaverage inflated surface. For example, I would like to display only the superiorfrontal and the posteriorcingulate. I tried to recreate the parcels myself by drawing labels, but they don't look pretty (see the attachment). I traced the labels in qdec (based on the Annotation/Opacity tab) and then I mapped them to fsaverage and visualized them with freeview. There's probably a better way to do that but I couldn't figure it out. Can anyone help me with this? Thanks! Mihaela

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dmri_motion tracula timepoint to timepoint motion, or timepoint to reference?
by Ruth Carper 15 Dec '15

15 Dec '15

Hi, I'm hoping to use the dmri_motion tool to quantify motion for some diffusion data that did not use the eddy_correct tool. We have registration matrices that we've successfully reformatted, but I've been scanning the FreeSurfer forum and see some conflicting information about whether the input to dmri_motion should reflect registration of each time point to a single reference orregistration of each time point to the preceding time point. i.e. t0-t1, t0-t2, t0-t3, .... vs. t0-t1, t1-t2, t2-t3, ... What input does dmri_motion expect? I think it's the former but the confusion arises from this post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41541.html5… ... Of our 4 motion measures, the rotation and translation are computed from the output of the eddy correction (which computes relative displacement from one volume to the next), and the intensity drop-out measures are computed from the raw uncorrected images (because the subsequent corrections will introduce some blurring and might lead to underestimation of the drop-out in each slice). So all measures are computed prior to B0 correction. Hope this helps, a.y But, the contents of the “eddy_correct” command appears to register each time point to a single reference time point. We’re using timepoint 1, i.e. b=0. From the text of Yendiki et al., 2013, I suspect that dmri_motion takes an input that is each timepoint to a single reference timepoint, but outputs a summary that is based on each timepoint to the immediately preceding timepoint? Can you clarify what input does dmri_motion expect? Thanks! Ruth Carper, PhDResearch Assistant Professor, SDSU

2 1

TRACULA NaN values in stats files and empty stats file
by denizzgursel 15 Dec '15

15 Dec '15

Dear Tracula users, I reconstructed uncinate fasciculus using the latest version of Freesurfer and Tracula. However, there seems to be a problem with produced stats files in dpath folder . I have -nan values for the center_avg variables in the file "pathstats.overall.txt" and there is no entry at all for the file "pathstats.byvoxel.txt", it is basically empty. Do you know why this could be happened? Files look like this: pathstats.overall.txt Count 1500 Volume 35 Len_Min 35 Len_Max 35 Len_Avg 35 Len_Center 0 AD_Avg 0.000935047 AD_Avg_Weight 0.000935047 AD_Avg_Center -nan RD_Avg 0.000682719 RD_Avg_Weight 0.000682719 RD_Avg_Center -nan MD_Avg 0.000766828 MD_Avg_Weight 0.000766828 MD_Avg_Center -nan FA_Avg 0.224986 FA_Avg_Weight 0.224986 FA_Avg_Center -nan pathstats.byvoxel.txt # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg # pathway end Thanks a lot for your help! -- D.

2 1

ERROR: Could not create directory
by jupiter 15 Dec '15

15 Dec '15

Hi, I am running freesurfer 6.0 beta with cuda 6.5 and FSL 5.0.9 on Linux platform, I've got following error: $ trac-all -path -c /scratchTRAC_TEST/dmrirc_first_exp_2.example ......... INFO: Found 8 baseline images (b = 0) out of a total of 136 frames INFO: Found 169534 voxels in brain mask INFO: Resolution of DWI space relative to base space is (1, 1, 1) Loading atlas reference volume from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Loading affine registration from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dmri/xfms/diff2mni.bbr.mat Loading segmentation map from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/aparc+aseg.nii.gz Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr ERROR: Could not create directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr Linux m2cvlnode17 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux The directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath is fully acceptable, I even tried manually create the directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, then run the command, it deleted /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, and never created it even the message was "Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr". Could it be a bug or could it be some thing I am missing? Appreciate clues to fix it. Thank you. Kind regards, - ju

2 1

TRACULA preprocessing error
by denizzgursel 15 Dec '15

15 Dec '15

Dear all, I am running Tracula preprocessing on NIFTI files. After running the command: trac-all -prep -c I get the error: ... processing /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_tmp0032 mv -f /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs.norot xfmrot /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi.ecclog /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs.norot /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs ln -sf /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi.nii.gz /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/data.nii.gz awk: fatal: cannot open file `1000' for reading (No such file or directory) mri_concat --i /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz --mean --o /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/lowb.nii.gz niiRead(): error opening file /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Nov 9 12:47:20 CET 2015 I checked the folder and 'dwi_frame.nii.gz' file was never created. I attached the trac-all.log file. Does anybody know how to solve this? Best, -- D.

3 4

Tracula - configuration file error
by L. Moreno-Lopez 15 Dec '15

15 Dec '15

Dear all, I am facing an error at the configuration file for trac-all. I am trying to run a single subject, for who there is a folder with all DWI DICOMs and a folder with the recon-all processing (Freesurfer 5.3). However, I am facing the following error, although no run list is specified. cs4$ export SUBJECTS_DIR=/scratch/lm618/tutorial_data/diffusion_recons cs4$ trac-all -prep -c /scratch/lm618/tutorial_data/diffusion_tutorial ERROR: run list is longer than subject list I'm attaching my configuration file. Any idea would be very much appreciate, Laura

2 1

Tracula Processing Question
by Douglas Merkitch 15 Dec '15

15 Dec '15

Hello FreeSurfer experts, We have a large dataset that was processed in FreeSurfer v 5.1 and we would like to run tracula on the dataset. Should we use the v 5.1 version of tracula to process the data? Or would it be acceptable/possible to use the v 5.3 tracula (with the v 5.1 processed T1 data)? Any advice or insight would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

2 1

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Freesurfer November 2015