Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 discussions

MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label
by DeCross, Stephanie N. 22 Apr '16

22 Apr '16

Hi, I’m trying to take an ROI in MNI152 volume space and make it into a cortical surface label, for visualization purposes. With my input being the lh thresholded, binarized MNI152 nii.gz label (when I visualize it, it looks as it should in fslview), I ran: mri_vol2vol -- mov <labelinput.nii.gz> -- targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz -- o <outputname.nii.gz> -- regheader -- talres 2 -- interp nearest mri_cor2label -- c <outputname.nii.gz from above> -- id 1 -- l ./<newoutputname.label> My commands above seem to have run fine, but when I open the lh in tksurfer and try to load the new lh label file, the dialogue runs for a little but then errors out: 12304 unassigned vertices in label - building spatial LUT… assigning vertex numbers to label... MatrixMultiply: m2 is null! And then tksurfer closes. I’m not sure what’s going wrong - does anyone have any pointers or troubleshooting methods I can try? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: (617) 724-3283 Fax: (617) 726-4078

2 7

Image geometries differ across time
by Lars M. Rimol 22 Apr '16

22 Apr '16

Hi, I'm running longitudinal recon-all (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 14.04.4, with three timepoints per subject. I get this warning about geometry (please see below). All three images have been converted from dicom to .mgz using mri_convert. From a previous question on the list from last year, I get the impression this warning should not appear if all images have been transformed the same way. I've pasted mri_info on both images at the bottom of the e-mail. The transformation matrices differ from timepoint to timepoint and I suspect this might be the reason for the warning. Is this a cause for concern? Thank you! #@# Longitudinal Base Subject Creation fr. 22. april 09:07:47 +0200 2016 /media/lmr2/subjects/TBI/artifakt_qc/KT5065_base mri_diff --notallow-pix /media/lmr2/subjects/TBI/artifakt_qc/Kt5065_2/mri/rawavg.mgz /media/lmr2/subjects/TBI/artifakt_qc/KT5065_1/mri/rawavg.mgz Volumes differ in geometry row=1 col=4 diff=1.606422 (1.60642) mri_diff --notallow-pix /media/lmr2/subjects/TBI/artifakt_qc/kt5065_reskann_2/mri/rawavg.mgz /media/lmr2/subjects/TBI/artifakt_qc/KT5065_1/mri/rawavg.mgz Volumes differ in geometry row=1 col=4 diff=1.713524 (1.71352) ******************************************************************************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ******************************************************************************* --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Comparison using mri_info [09:27 lmr@dmed4870] > mri_info KT5065_1/mri/orig/001.mgz Volume information for KT5065_1/mri/orig/001.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -0.5000 : x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0000 -0.0000 -1.0000 87.5000 -1.0000 -0.0000 -0.0000 128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.0000 -1.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -1.0000 0.0000 0.0000 87.5000 0.0000 0.0000 0.0000 1.0000 [09:27 lmr@dmed4870] > mri_info Kt5065_2/mri/orig/001.mgz Volume information for Kt5065_2/mri/orig/001.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -2.1064 : x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a = -3.2129 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -5.6225 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0000 -0.0000 -1.0000 85.8936 -1.0000 -0.0000 -0.0000 124.7871 0.0000 -1.0000 0.0000 122.3775 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.0000 -1.0000 -0.0000 124.7871 -0.0000 -0.0000 -1.0000 122.3775 -1.0000 0.0000 0.0000 85.8936 0.0000 0.0000 0.0000 1.0000 [09:28 lmr@dmed4870] > mri_info kt5065_3/mri/orig/001.mgz Volume information for kt5065_3/mri/orig/001.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = 1.2135 : x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a = 8.4827 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -11.9426 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0000 -0.0000 -1.0000 89.2135 -1.0000 -0.0000 -0.0000 136.4827 0.0000 -1.0000 0.0000 116.0574 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.0000 -1.0000 -0.0000 136.4827 -0.0000 -0.0000 -1.0000 116.0574 -1.0000 0.0000 0.0000 89.2135 0.0000 0.0000 0.0000 1.0000 sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

2 1

AAL 3D rendering with subcorticals
by João V. Dornas 21 Apr '16

21 Apr '16

Dear friends, I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html) My problem is the following. When I execute this command: mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L specifically for the ROI Pallidum, a subcortical ROI, I receive the following error $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.Colin27_aal2std.mgh Loading /Applications/freesurfer/subjects/FS_spm_CanonicalBrain/surf/lh.white Scanning the volume Found 0 label voxels ERROR: found no voxels matching id 75 This happens both for Pallidum Left and Pallidum Right, but all other AAL ROI work fine. I have an almost complete 3D rendering for my AAL. Only these subcortical regions are missing. Someone knows what could be happening? Thanks for the help. best, -- João V. Dornas Phd student in Neuroscience Cognitive Biology Group, Institute of Biology Otto von Guericke University, Magdeburg Germany

4 9

lme model for within-subjects repeated measures design
by martina.papmeyer＠puk.unibe.ch 21 Apr '16

21 Apr '16

Dear FreeSurfer experts I have one question regarding my data analysis and would be extremely thankful for any advice! My data-set is as follows: I have repeated measures (time point 0 (T0), time point 1 (T1)) of several subjects. All individuals underwent an intervention at one of the time points and a placebo condition at the other time point in a fully randomized fashion. Thus, half of the subjects received treatment at T0 and half of them at T1. I am interested in the putative effect of the intervention on cortical thickness in a ROI. A major challenge is that the time between T0 and T1 varies between individuals and that I expect the time to impact on my dependent variable and to likely interact with the condition (treatment versus placebo). I thought about conducting a simple repeated-measures ANOVA. However, as stated, I want to take the time between the two sessions into account. I also thought about an analysis of rates or percent changes. However, this approach does not model the correlation among the repeated measures and is thus associated with a reduction in power. Accordingly, I am trying to use lme models to analyse my data. Since I have no between-group variable but a within-subjects design, I am concerned if my thoughts are correct and would be grateful for feedback. I ran the longitudinal FS stream and followed the longitudinal lme model tutorial. I propose the following lme model with one random factor: thickness = intercept (random factor) + time since baseline + ICV + condition (placebo or treatment) + timeXcondition + Age (does not change across time interval) + gender The analysis finishes with 0% non-covergence. Can you tell me if my model is suitable given the fact that it is a within-subjects design? I also started wondering if it was possible to model time as a random factor but I think that I read that this is not suitable if you only have two groups (in my case: conditions). Thank you very much for help and advice! All best wishes, Martina Universitäre Psychiatrische Dienste Bern (UPD) Universitätsklinik für Psychiatrie und Psychotherapie Systemische Neurowissenschaften der Psychopathologie Zentrum für Translationale Forschung Dr. phil. Martina Papmeyer, Wissenschaftliche Mitarbeiterin Bolligenstrasse 111, CH-3000 Bern 60 Tel: ++41 0(31) 930 9599, Fax: ++41 0(31) 930 9961 Mail: Martina.Papmeyer(a)puk.unibe.ch www.puk.unibe.ch

3 3

white matter edits not incorporated
by dgw 21 Apr '16

21 Apr '16

Hi, I recently edited a brain with a gyral cyst, carefully filling the cyst with white matter in the wm.mgz. Unfortunately after running: /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 none of the edits were incorporated. Is the FLAIRpial flag incompatible with autorecon2-wm? Is there some other misake? I followed this guide https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freev… Thanks, Dan

3 11

Qdec interface issue
by Sahil Bajaj 21 Apr '16

21 Apr '16

Hello, I am working on measuring cortical thickness of a patient group. I am using Ubuntu 14.04 Somehow, if I use command line to perform the analysis, Freesurfer/qdec is working fine but if I use Qdec interface, it works fine initially but when I switch to display window, it doesn't allow me to change/edit FDR p-values, threshold min and max, although I can click on all the options on display window e.g. inflated, pial, white, etc. Also, when I tried to do the same on other computer (Mac), it works fine for me. I was wondering if this is because of video card problem or something. The thing is it was working before for some time, then after a computer crash, it no longer works. We replaced the video card but are still experiencing the same problem. At this point I would welcome any suggestions. Thanks, Sahil -- -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

1 0

"Bump" - Fwd: lGI value is aberrantly high and misalignment fix
by Marco Bucci 21 Apr '16

21 Apr '16

I forward again my email, that has not been sent to the mailing list yet. ---------- Forwarded message ---------- From: Marco Bucci <bucci.marco(a)gmail.com> Date: 2016-03-22 10:05 GMT+02:00 Subject: Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Dear Marie and Freesurfer Users, thanks for your support. I could not imagine that freeview was visualizing wrongly the surfaces. For this reason, my colleague and I have added a small "integrity check" with which we compare the min and max of the vertexes coordinates of pial and pial-outer. If the pial min and max are closer to the center it means that pail is included in the outer surface. We believe this is faster than checking visually with the viewer all the surfaces, slice by slice. The subject surfaces of which I sent you the recon.log passed the test. But... I ran another case and unfortunately it did not pass the check. I attach the recon log, the screenshot of tkmedit with lh.pial going below the outer surface. Is it important for the lgI calculation purposes? I also attach the Matlab code for the testing (it is rough, but works) It is possible to check with a stepsize of 1 to be absolutely sure about any intersection, but it takes longer time. Looking forward to hear from you soon. Thanks in advance for your help Yours, Marco (and Harri) P.S. I went back to the original line 51 of the Marie Schaer code in "make_outer_surface". No "fix" anymore. 2016-03-17 23:19 GMT+02:00 Marie Schaer <Marie.Schaer(a)unige.ch>: > > Hi Marco, > > It’s pretty strange because from the recon-all.log you sent, the first LGI > process went fine (line 14584 and 19329 for the right and left hemispheres, > on Dec 15). Then you don’t run anything else on the surfaces and just > reprocess the exact same LGI process for the same subject (Dec 18), and you > get different values from what you just had, with many values <1, plus it > gets stuck. > > Could that be related to your change on line 51 in make_outer_surface? > When you say misalignment, do you mean in freeview or tkmedit? Because we > saw some occurrences of misalignment in freeview, which indeed are related > to the surface format and as long as the surfaces align well in tkmedit > then you should definitely not change anything in the make_outer_surface > code. > > Keep me posted, > > Marie > > > On 16 Mar 2016, at 02:51, Marco Bucci <bucci.marco(a)gmail.com> wrote: > > Dear all, > > I forward again my original post. > I also attach the recon-all.log of one of the several faulty cases. > > I run freesurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0) > in Mac OS X 10.9.4 and -lgI option with Matlab_R2013a > and I have fixed the SearchProjectionOnPial.m. > > I also had to fix line 51 of make_outer_surface.m > "v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the > different orientation" > with > "v2=[vol.vox2ras1(1,4)-v(:,1) v(:,3)+vol.vox2ras1(2,4) > vol.vox2ras1(3,4)-v(:,2)];" > in order to use the image coordinate to fix surface orientation and > alignment. > > If I would use the original line 51, the surface produced by recon -lgi > results > misaligned with the reference pial and image. > > My problems remains the aberrantly high lgI value in most of my subject > images. > > Can you help me? > > Yours, > Marco Bucci > > > ---------- Forwarded message ---------- > From: Marco Bucci <bucci.marco(a)gmail.com> > Date: 2015-12-22 23:49 GMT+02:00 > Subject: Re: [Freesurfer] lGI value is aberrantly high > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > > Dear all, > > I have a problem with the LGI module. > At the step when the software computes the LGIs for the vertices, > In one vertex the lGI results aberrantly high and the software exits > with ERRORS. > > I tried the solution suggested by Marie Schaer to rereconstruct > The images with "randomness" > Recon-all -autorecon2-wm -randomness -autorecon3 > > I tried this fix on two of my subjects > With errors. Not all subject resulted > Errors in the computation of the gyrification. > > Can you help me? > > Marco Bucci > Turku Pet Center > > Sent from my iPhone > > > > -- > **************************************************** > Marco Bucci, PhD in > Clinical Physiology and Nuclear Medicine > Turku PET Centre > Turku University Central Hospital (TUCH) > PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland > tel. +358 2 3132798 > fax. +358 2 2318191 > mobile: +358 40 6873976 > UTU e-mail: marbuc(a)utu.fi > **************************************************** > <recon-all.log>_______________________________________________ > 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 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. > > -- **************************************************** Marco Bucci, PhD in Clinical Physiology and Nuclear Medicine Turku PET Centre Turku University Central Hospital (TUCH) PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland tel. +358 2 3132798 fax. +358 2 2318191 mobile: +358 40 6873976 UTU e-mail: marbuc(a)utu.fi **************************************************** -- **************************************************** Marco Bucci, PhD in Clinical Physiology and Nuclear Medicine Turku PET Centre Turku University Central Hospital (TUCH) PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland tel. +358 2 3132798 fax. +358 2 2318191 mobile: +358 40 6873976 UTU e-mail: marbuc(a)utu.fi ****************************************************

1 1

identity.nofile
by Trisanna Sprung-Much 20 Apr '16

20 Apr '16

Hi All! Could someone please tell me how to run mri_vol2surf using identity.nofile as the transformation? I cannot find any documentation on identity.nofile Additionally, if my next step is to use the output of mri_vol2surf in mri_cor2label, which takes surface overlays OR volumes, what format should my output be for mri_vol2surf? many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

4 18

Preprocessing task data with multiple B0-corrected runs
by Shea, Conor 20 Apr '16

20 Apr '16

Dear Doug, I'm trying to use FSFAST to analyze task data with multiple runs. Before using the preproc-sess pipeline, I ran B0 correction on each of the runs, so I have 3 different b0dcmap files. I'm trying to figure out the best way to run preprocessing on the three runs simultaneously using preproc-sess, but I don't know how to get FSFAST to use each run's specific b0dcmap in the preprocessing of each run's data. FSFAST wants the b0dcmap files to be in the task folder, but how can it differentiate between the three b0dcmap files if they're not in the run folders? Thanks, Conor

2 5

Functional Connectivity with Hippocampal Subfields as seeds
by Julio Alberto González Torre 20 Apr '16

20 Apr '16

Hi Freesurfers. As I'm currently performing the Funcional Conectivity workflow with FSFAST, the 4th step requires me to choose the areas to use as seeds. I would like to use the hippocampal subfields as seeds, but I can't select them because the aparc+aseg.mgz doesn't contains those labels. The only area available is the whole hippocampus, which implies a huge seed that doesn't discriminate the subfields, and I'm interested in exploring if there are conectivity differences between the subfields. Is there any way to create the seeds for each subject using the hippocampal subfields as reference? Thanks a lot.

2 1

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Freesurfer April 2016