Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30098 discussions

segmentation errors in subject with severe atrophy
by Corinna Bauer 09 Feb '16

09 Feb '16

Dear all, We are working on editing the segmentation of a subject with severe atrophy due to a seizure event that occurred during infancy. In portions of the parietal and frontal lobe the atrophy is so severe that freesurfer can't find any WM or GM. Is there a way to manually fill in the GM so that it is captured within the surfs? Because we have other modalities that use the Desikan atlas, this is an important first step. I have attached a few figures for examples. Thanks!!

1 0

retinotopy analysis: wedge position, angle offset, tksurfer
by Kinga Littke 09 Feb '16

09 Feb '16

Hello everyone, I've analyzed my polar retinotopy data (2 runs with clockwise and counterclockwise wedge rotations) using FsFast. To better understand the analysis, I'd be very grateful if you could help me with the following questions: 1. I understand that freesurfer assumes that the rotating wedge starts at 12 o'clock, which means that the middle of the wedge has to be exactly aligned with the upper vertical meridian. Is that correct? In my task I used a 45 degree wedge that starts rotating with its left and right borders aligned to to 12 o'clock, respectively. Do I need to account for that somehow in the analysis or in the display of the results, for example by changing the angle offset while displaying the polar map (under: view -> configure -> Phase encoded data display)? 2. When searching through the archive, I came across this thread below about freesurfer assuming that a clockwise rotating wedge starts at 12:00 and a counterclockwise one at 15:00: *[Freesurfer] polar angle analysis with clockwise- and counterclockwise-rotating wedges* * Thomas Janssens thomasj at nmr.mgh.harvard.edu <freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20polar%20angle%20analysis%20with%20clockwise-%20and%0A%09counterclockwise-rotating%20wedges&In-Reply-To=%3CE0168CFF-41F9-4FE3-944B-29E5F6E2FAAC%40nmr.mgh.harvard.edu%3E> Mon Aug 13 08:24:37 EDT 2012* *Hi Doug, It seems that, our stimulus presentation is inconsistent with the way freesurfer processes the retinotopy clockwise and counter clockwise data. After going through the freesurfer code I found the following. The freesurfer code assumes that the wedge starts horizontally for both clockwise and counterclockwise runs. In the glm analysis, the difference between the two types of runs (specified in the paradigm file by "neg" or "pos") is programmed in the function $FREESURFER_HOME/fsfast/toolbox/flac_desmat.m as follows: for "pos" runs the real part equals cos(phz) and the imaginary part equals sin(phz) for "neg" runs the real part stays cos(phz) and the imaginary part equals -sin(phz). This is correct if the wedge starts in the horizontal positionm, but not if the wedge starts vertically. In that case the code above will lead to a phase shift of half a cycle for the "neg" runs compared to the "pos" runs. However, this problem is solved by changing the code for the "neg" runs to: the real part equals -cos(phz) and the imaginary part equals sin(phz). This small change fixed the problems for our data. Thomas* Should I also make the same adaptation, i.e. inverse the signs of sin and cos for negative runs in my analysis for my retinotopy analysis, given that in freesurfer v. 5.3, in flac_desmat.m file, the "pos" and "neg" runs are still specified as cos(phz), sin(phz) and cos(phz) and -sin(phz), respectively. 3. When displaying the results using rtview command, I see somewhat blurred retinotopic maps, whereas I do not use any smoothing in the analysis (mkanalysis-sess [...] - fwhm 0). I've noticed that one of the output message in terminal while running tksurfer is the following: tksurfer: polar-views.tcl: read and smooth real Fourier comp, surfer: smooth_val(2)? Is it possible that tksurfer smooths the maps before displaying them? If so, how to display unsmoothed results? rtview command I use to display polar maps on the left hemisphere: rtview --s subjNr --lh --polar \ --real subjNr/bold/rtopy.self.lh/polar/real.nii.gz --imag subjNr/bold/rtopy.self.lh/polar/imag.nii.gz --fsig subjNr/bold/rtopy.self.lh/polar/fsig.nii.gz Thank you very much for your help, Kinga Littke

1 0

Gray matter intensity
by Sabrina Yu 08 Feb '16

08 Feb '16

Hello, I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html> And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity. 1) Does the wmparc.stats contain mean white matter intensity values for each ROI? 2) Is it possible to extract these same mean intensity values for gray matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data. Thank you, Sabrina Yu

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R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 08 Feb '16

08 Feb '16

Thanks.I have down a right ad left ROI on the surface.Next, I have run: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gzmri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgzmri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.configfcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config but during fcseed-sess this error occurs: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user StefanoUseRobust 0Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gzLoading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gzVoxel Volume is 64.5752 mm^3Generating list of segmentation idsFound 1 segmentationsComputing statistics for each segmentation 0 1 0 0.000MRIalloc(0, 1, 1): bad parmReporting on 0 segmentationsComputing spatial average of each frameWriting to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mghSegmentation fault ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 8-feb-2016 4.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, stdp82(a)virgilio.it wrote: Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer. How can I do it? Should I use mri_label2vol? Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

tkregister2 - horizontal and coronal inverted in the functional only
by Ilaria Sani 08 Feb '16

08 Feb '16

Dear All, I have a functional and a T1 registered, but they are not in anatomical coordinates. I put the anatomical in the desired position by using tkregister2. I was hoping to use the output reg file to re-position the functional as well. I got an unexpected output! The functional looks reoriented BUT, coronal is horizontal, horizontal is coronal and sagittal is 90deg rotated. How did it happen and how can I fix the problem? Thanks, Ilaria

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matrix is ill-conditioned or badly scaled, condno = 27492.1
by Nabin Koirala 07 Feb '16

07 Feb '16

Dear Freesurfer forum, 'I am trying to run qdec analysis for a group of subjects to see if correlation exists but I am getting this error only for this particular set of data but could not figure out what is exactly wrong with it. Your suggestion would be greatly appreciated. Following is the terminal output for the process: .......... Saving design matrix to /g/f/h/s/freesurfer/subjects/qdec/Untitled/Xg.dat Normalized matrix condition is 27492.1 Design matrix ------------------ 1.000 0.408; 1.000 0.417; 1.000 0.417; 1.000 0.405; 1.000 0.412; 1.000 0.412; 1.000 0.411; 1.000 0.417; 1.000 0.405; 1.000 0.406; 1.000 0.402; 1.000 0.419; 1.000 0.413; 1.000 0.413; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 27492.1 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat Many thanks in advance. Regards, Nabin

3 5

mri_vol2surf Averaging with exclusion of specific values
by Gardumi Anna (PSYCHOLOGY) 07 Feb '16

07 Feb '16

Dear FreeSurfer expert, I would like to project my maps from the "original" functional space (2.5mm iso, same format as COPE images from FSL) to inflated FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all pipeline) excluding voxels with a specific value (e.g. 0) from the averaging procedure of the projection. The reason for this is that I have non-continuous maps (i.e. map values are defined only for some voxels; voxels for which map value is not defined will have 0 as value). Is there a way to perform the projection excluding voxels with a specific value from the averaging of the projection? Thank you in advance for any help! Anna As complementary information: My maps have discrete values (between -10 and 10) and at the moment I am using the following command: mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap _InFS_projAvg02_SurfLh.mgh However, in this way the resulting surface map will have values biased by including in the average also the 0 values which in reality represents voxels not included in the map.

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selxavg3-sess problem: SVD input matrix contains NaN
by Mcnorgan, Christopher 07 Feb '16

07 Feb '16

Hi, I'm attempting an inaugural run through the FS pipeline on some event-related data collected over 6 runs. I'm not sure if this makes any difference, but the experiment is self-paced, and the events are of varying duration (it's a lexical decision task, and participants can take up to 4 seconds to respond but typically respond between 600 - 800ms, with an exponentially-decreasing jittered ITI between trials). When I run selxavg3-sess on this single participant, the following error is generated: /********************************** Saving X matrix to /home/kali/fMRI/LDT/1001_001/bold/LDT.sm6.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n *******************************************/ If I open up the generated .mat file, I see the several rows/columns of the XtX matrix are indeed populated with NaN. We tried running the mkanalysis-sess a couple different ways, getting the same error, though our different parameter selections for mkanalysis-sess lead to different XtX matrices, so I suspect that this might be the source of the problem. Unfortunately, I have no insight into what the root of the problem might be. The .par files used have the event durations set to the reaction times for each trial, and the -refeventdur value is set to the mean reaction time Thanks for any help anyone might be able to give me

2 1

generate .mgz file from DICOM
by Kan Ding 07 Feb '16

07 Feb '16

Hi, I am having trouble to generate .mgz file from DICOM. However, I was able to run the same code with NIFTI file. What did I do wrong? Thanks for your help. Kan NUA502608:300T1 kding$ ls 30100000-0.dcm 30100000-27.dcm 30100000-1.dcm 30100000-28.dcm 30100000-10.dcm 30100000-29.dcm 30100000-100.dcm 30100000-3.dcm 30100000-101.dcm 30100000-30.dcm 30100000-102.dcm 30100000-31.dcm 30100000-103.dcm 30100000-32.dcm 30100000-104.dcm 30100000-33.dcm 30100000-105.dcm 30100000-34.dcm 30100000-106.dcm 30100000-35.dcm 30100000-107.dcm 30100000-36.dcm 30100000-108.dcm 30100000-37.dcm 30100000-109.dcm 30100000-38.dcm 30100000-11.dcm 30100000-39.dcm 30100000-110.dcm 30100000-4.dcm 30100000-111.dcm 30100000-40.dcm 30100000-112.dcm 30100000-41.dcm 30100000-113.dcm 30100000-42.dcm 30100000-114.dcm 30100000-43.dcm 30100000-115.dcm 30100000-44.dcm 30100000-116.dcm 30100000-45.dcm 30100000-117.dcm 30100000-46.dcm 30100000-118.dcm 30100000-47.dcm 30100000-119.dcm 30100000-48.dcm 30100000-12.dcm 30100000-49.dcm 30100000-120.dcm 30100000-5.dcm 30100000-121.dcm 30100000-50.dcm 30100000-122.dcm 30100000-51.dcm 30100000-123.dcm 30100000-52.dcm 30100000-124.dcm 30100000-53.dcm 30100000-125.dcm 30100000-54.dcm 30100000-126.dcm 30100000-55.dcm 30100000-127.dcm 30100000-56.dcm 30100000-128.dcm 30100000-57.dcm 30100000-129.dcm 30100000-58.dcm 30100000-13.dcm 30100000-59.dcm 30100000-130.dcm 30100000-6.dcm 30100000-131.dcm 30100000-60.dcm 30100000-132.dcm 30100000-61.dcm 30100000-133.dcm 30100000-62.dcm 30100000-134.dcm 30100000-63.dcm 30100000-135.dcm 30100000-64.dcm 30100000-136.dcm 30100000-65.dcm 30100000-137.dcm 30100000-66.dcm 30100000-138.dcm 30100000-67.dcm 30100000-139.dcm 30100000-68.dcm 30100000-14.dcm 30100000-69.dcm 30100000-140.dcm 30100000-7.dcm 30100000-141.dcm 30100000-70.dcm 30100000-142.dcm 30100000-71.dcm 30100000-143.dcm 30100000-72.dcm 30100000-144.dcm 30100000-73.dcm 30100000-145.dcm 30100000-74.dcm 30100000-146.dcm 30100000-75.dcm 30100000-147.dcm 30100000-76.dcm 30100000-148.dcm 30100000-77.dcm 30100000-149.dcm 30100000-78.dcm 30100000-15.dcm 30100000-79.dcm 30100000-150.dcm 30100000-8.dcm 30100000-151.dcm 30100000-80.dcm 30100000-152.dcm 30100000-81.dcm 30100000-153.dcm 30100000-82.dcm 30100000-154.dcm 30100000-83.dcm 30100000-155.dcm 30100000-84.dcm 30100000-156.dcm 30100000-85.dcm 30100000-157.dcm 30100000-86.dcm 30100000-158.dcm 30100000-87.dcm 30100000-159.dcm 30100000-88.dcm 30100000-16.dcm 30100000-89.dcm 30100000-160.dcm 30100000-9.dcm 30100000-17.dcm 30100000-90.dcm 30100000-18.dcm 30100000-91.dcm 30100000-19.dcm 30100000-92.dcm 30100000-2.dcm 30100000-93.dcm 30100000-20.dcm 30100000-94.dcm 30100000-21.dcm 30100000-95.dcm 30100000-22.dcm 30100000-96.dcm 30100000-23.dcm 30100000-97.dcm 30100000-24.dcm 30100000-98.dcm 30100000-25.dcm 30100000-99.dcm 30100000-26.dcm NUA502608:300T1 kding$ recon-all -i 30100000-0.dcm -s 300 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/kding/desktop/data/TBIE/TBIET1/300T1 Actual FREESURFER_HOME /Applications/freesurfer Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 /Users/kding/desktop/data/TBIE/TBIET1/300T1/300 \n mri_convert /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz \n mri_convert /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm... Starting DICOMRead2() dcmfile = /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm dcmdir = /Users/kding/desktop/data/TBIE/TBIET1/300T1 WARNING: tag ImageNumber not found in /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm WARNING: tag image orientation not found in /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm Ref Series No = 18976 ERROR: bits = 0 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 recon-all -s 300 exited with ERRORS at Thu Feb 4 15:53:19 CST 2016 For more details, see the log file /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 1

Volume analysis in native space vs. mni305 space
by Rodriguez-Thompson, Anais 07 Feb '16

07 Feb '16

Hi FreeSurfer experts, I'm in the process of switching over our first-level analyses from being run in native space to being run in fsaverage/mni305 space. Looking at the first-levels on an individual subject level, the volume analyses look fairly different (cortical signal especially is lost in the mni305 analysis). I've attached a couple of slides with images comparing the two volume analyses. My commands for the mni305 analysis are... Pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -d $SUBJECTS_DIR -fsd bold -so siemens Mkanalysis: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2 -fwhm 5 -paradigm slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -per-run -TR 2 -stc siemens -force Mkcontrast: mkcontrast-sess -analysis SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -contrast 2vFix -a 2 -c 0 My commands for the native space analysis are... Preprocessing: preproc-sess -s GDDA001 -fwhm 5 -per-run -d $SUBJECTS_DIR -fsd bold Mkanalysis: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 Mkcontrast: mkcontrast-sess -analysis SIRP_LoadRegression_Stable5_050514 -contrast 2vFix -a 2 -c 0 I have a couple of questions regarding the differences between the two analyses. First, why is so much of the signal robustness from the native space volume analysis lost in the mni305 analysis? Second, why are the voxel sizes so different between the two analyses (with the native space analysis having a much larger voxel size)? Thanks, Anais

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