[Freesurfer] CVS registration questions
Hi Lilla et al, I am preparing to CVS register 30+ subjects to improve FSL probabilistic tractography alignment across subjects. First, thanks for a really cool tool! Then, I have some questions: 1. mri_cvs_register step1 is spherical registration. However, I have already run FS5.3 recon-all -all for all subjects, which includes spherical registration. Are the recon-all and mri_cvs_register spherical registrations identical? If so, will mri_cvs_register be able to use the previously computed spherical registration (with flags --step2 --step3), or will it need to compute a new spherical registration? Will mri_cvs_register overwrite any of my earlier recon-all results? 2. What are the pros and cons for using one of the following as templates, and which one would you recommend: -Randomly selected individual subject -CVS35 -CVS35_inMNI152 3. When using MNI152_1mm as template, I guess this is a 1 mm resolution image (as $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/T1.mgz seems to be in 1 mm resolution)? Technically, is this the cvs_avg35 image that has been CVS-registered with the MNI152_1mm image? Or is this a FLIRT-type 3D registration from cvs_avg35 to MNI152_1mm without surface information (I guess extracting the surface from MNI152 would be difficult)? 4. I run into the following error in FS stable 5.3 (source /usr/local/freesurfer/nmr-stable53-env): mri_cvs_check --mov $SUBJECT Using the CVS template as registration target. The following files are missing: /usr/local/freesurfer/stable5_3_0/bin/mri_cvs_register.settings.txt You need to find these files or run reconall on the data in order to run mri_cvs_register. Is this file required, or is this a bogus error? 5. Are there parallel processing versions that could be run on the cluster? Thanks! Tommi --- Tommi Raij, MD, PhD TM Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] CVS registration questions
Thanks Lilla! Which MNI152 version was used as template when doing nonlinear CVS-registering from cvs_avg35 into MNI152 space? For example, was this MNI152 ICBM 2009a 1mm Nonlinear Asymmetric? Bests, Tommi > > Hi Tommi, > > >> I am preparing to CVS register 30+ subjects to improve FSL probabilistic >> tractography alignment across subjects. First, thanks for a really cool >> tool! Then, I have some questions: >> >> 1. mri_cvs_register step1 is spherical registration. However, I have >> already run FS5.3 recon-all -all for all subjects, which includes >> spherical registration. Are the recon-all and mri_cvs_register spherical >> registrations identical? If so, will mri_cvs_register be able to use the >> previously computed spherical registration (with flags --step2 --step3), >> or will it need to compute a new spherical registration? Will >> mri_cvs_register overwrite any of my earlier recon-all results? > > The two calls are similar but not identical. In the recon call your > registration target is different and the call uses a different set of > parameters. So you should still call step1 in your processing and no > worries, CVS does not overwrite your previous solutions. > >> 2. What are the pros and cons for using one of the following as >> templates, >> and which one would you recommend: >> -Randomly selected individual subject >> -CVS35 >> -CVS35_inMNI152 > > That is your call and the decision will probably depend on your > application or intended use of the results. Using an individual subject > as a template can bias further population comparison, for example, as the > subject might not be the most representative one for your population. > Using the CVS35 atlas diminishes this bias and the CVS35_inMNI152 would > provide you with results in the MNI152 space, so if you need to report > results in that space that could be useful. > >> 3. When using MNI152_1mm as template, I guess this is a 1 mm resolution >> image (as $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/T1.mgz seems >> to >> be in 1 mm resolution)? Technically, is this the cvs_avg35 image that >> has >> been CVS-registered with the MNI152_1mm image? Or is this a FLIRT-type >> 3D >> registration from cvs_avg35 to MNI152_1mm without surface information (I >> guess extracting the surface from MNI152 would be difficult)? > > It is the CVS35 average transformed and reconned in the MNI152 space. It > definitely has surface information, otherwise CVS would not run. > >> 4. I run into the following error in FS stable 5.3 (source >> /usr/local/freesurfer/nmr-stable53-env): >> >> mri_cvs_check --mov $SUBJECT >> Using the CVS template as registration target. >> The following files are missing: >> /usr/local/freesurfer/stable5_3_0/bin/mri_cvs_register.settings.txt >> You need to find these files or run reconall on the data in order to run >> mri_cvs_register. >> >> Is this file required, or is this a bogus error? > > That file is required. I will double-check why that is not in the > distribution. > >> 5. Are there parallel processing versions that could be run on the >> cluster? > > Yes. You can use --openmp to take adventage of it. The default is 1. > > Let me know if you have any other questions. Lilla > > > ___ Freesurfer mailing list Freesurfer@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] tksurfer partial overlays?
Hi, We need to display surface data (.w file). However, our algorithm failed to assign values for some vertices (and were therefore given the value of exactly zero), and to clearly differentiate those from vertices where we successfully computed values, we would like the vertices where we could not compute a value to be blank (=only the underlying anatomical surface shows). Normally I would just threshold the values to get rid of the "blank" vertices. However, we want to use tksurfer "offset 0.5" to shift the distribution such that all values smaller than 0.5 are shown as blue and all values larger than 0.5 in red/yellow. The offset also has the effect that the vertices where we were unable to compute a value will now have a value of exactly -0.5. Then, the question becomes how to make tksurfer paint only the vertices where we have a successfully computed value. After the shift, thresholding will no longer work because it only operates on values around zero. We have tried editing the .w file by both (i) removing the values from the vertices that we do not want painted, and (ii) removing the vertices (the entire line, vertex index plus value) from the file, but the tksurfer brain surface window still shows an overlay with a value of 0 in these vertices. Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] Averaging overlays/labels across subjects
Dear Surfers, I have (non-fMRI) .w format surface overlays/labels, computed at the smoothwm surface in each individual subject, in 25 subjects. FS5.1 recon-all has been run for all T1 images. I already managed to convert all individual surface overlays into the surface space of one of the subjects (or fsaverage) using mri_surf2surf, and in the process also converted the format from .w to .mgh (as I understand .w is pretty much legacy). Now, I would just need to compute an average across these overlays. I would greatly appreciate any suggestions which FS tools to use for this. Thank you in advance! (In case it matters, the overlays are E-field estimates, with a numerical value given for each vertex point. Also each overlay has only one time point.) Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] mni152reg error (file permission denied)
Dear Surfers, mni152reg --$SUBJECT exits with the error: mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402': Permission denied Thereafter, a couple consequential errors follow ... niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii ... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii This is on FS 5.1.0 stable. The error seems linux box independent. Please let me know if you need further info. Thanks! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] FS 5.1 MNI305 aparc+aseg registration with FSL MNI152
Dear fellow Surfers, I am trying to overlay FreeSurfer 5.1 MNI305 (=fsaverage) aparc+aseg.mgz 3D volumes (caudate, putamen, pallidum, etc) onto FSL MNI152 2mm resolution volume. I first extract the nuclei from MNI305 aparc+aseg.mgz, for example: mri_extract_label $FREESURFER_HOME/subjects/fsaverage/mri/aparc+aseg.mgz 11 MNI305_3D_masks/mask_lh_caudate.nii I then try to resample the extracted volume into FSL MNI152 2mm space, using the registration that comes with FS 5.1 (.dat format): mri_vol2vol --mov MNI305_3D_masks/mask_lh_caudate.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o MNI152_3D_masks/mask_lh_caudate.nii Unfortunately, caudate appears in a clearly incorrect location, both when checking the result with tkmedit2, and when viewing the volumes with freeview. Adding --inv does not fix this either. However, if I simply overlay the volume extracted from MNI305 aparc+aseg on the FSL MNI152 2 mm volume, the location looks just fine. It therefore appears that MNI305 and MNI152 are in the same space, and mri_vol2vol is not needed. Is this correct? Or am I just using an incorrect register.dat file? Thanks! Tommi Details: On machine ernie nmr-std-env (5.1.0 stable) $FSLDIR = /usr/pubsw/packages/fsl/current/ $FREESURFER_HOME = /usr/local/freesurfer/stable5_1_0/ --- Tommi Raij, MD, PhD TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] dmri_trk2trk issue
Hi,
I am attempting to morph deterministic tractography results (.trk file)
from the individual diffusion space into the average brain
cvs_avg35_inMNI152. However, something goes wrong, as the output trk file
is greatly misplaced / strongly distorted / wrongly sized.
The input file (dsi60.trk, a TrackVis trk file with an angle threshold of
60 degrees) loads fine in Trackvis, as do the inref and outref volumes (in
.nii format). The rigid body (.mat) and nonlinear (.m3z) registrations
also appear ok. The mat file (or more precisely, the corresponding
register.dat file) looked fine with tkregister2 and the latter was
successfully used to morph the corresponding probabilistic tractography
results from the individual diffusion space to cvs_avg35_inMNI152 (= the
same transformation I am trying to do here).
Any suggestions what I am doing wrong? For example, could this be related
to inref/outref voxel sizes or coordinate systems?
Just in case, I already tried using the inverse rigid registration
(anat2diff.mat) and the FDT-generated files inside DSI.bedpostX/xfms
(diff2str.mat and its inverse) but the results were in all cases very much
wrong, just in different ways.
FS 5.3 (nmr-std-env)
on machine avml
cd $SUBJECTS_DIR
dmri_trk2trk \
--in $SUBJECT/DSI/dsi60.trk \
--out TMSDSIGA_19Jul14/${SUBJECT}inCVS35MNI152_dsi60.trk \
--inref $SUBJECT/mri/norm.mgz \
--outref $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \
--reg $SUBJECT/DSI/${SUBJECT}_diff2anat.mat \
--regnl $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \
reg (.mat) was computed as follows:
bbregister --mov dsi_b0.nii --frame 0 --bold --s $SUBJECT --init-fsl --reg
DSIregister.dat --fslmat ${SUBJECT}_anat2diff.mat
I would be happy to copy the data to a location of your choosing if you
would like to replicate the error. Thanks!
Tommi
---
Tommi Raij, MD, PhD
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th St
Charlestown, MA 02129
U.S.A.
___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5
Hi, Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use the "noveau" drivers that come with CentOS 6.5 or would it be better to go with the proprietary drivers from NVIDIA? I would imagine that since FS 5.3 does not use GPU for analysis, this is mainly relevant for visualization (freeview etc) requiring 3D rendering of volumes, surfaces, and tractography results simultaneously. In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here. Thanks! Tommi --- Tommi Raij, MD, PhD ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FreeSurfer NVIDIA card drivers with CentOS 6.5
Hi Dan, Thanks. While I agree that all kinds of GPUs might be sufficient as far as the hardware and FS computations go, the drivers in fact make a major difference for visualizations. For my card the proprietary NVIDIA drivers turned out to be 10-20 times faster than the CentOS 6.5 Noveau drivers. For example freeview with a couple of layers and little bit of 3D rendering is unusable with the Noeveau drivers and works like a charm with the NVIDIA drivers - the difference is really like day and night. Cheers, Tommi > Just to add. If you are not using the CUDA options (which in my > understanding aren't being updated anyway), I find that the gpu > included in modern Intel cpus is more than sufficient for my > FreeSurfer and MNE uses. > > > HTH > D > > On Fri, Aug 22, 2014 at 4:15 PM, Z K wrote: >> Tommi, >> >> Here at the Martinos Center we use the proprietary drivers from NVIDIA. >> We have no reasons to believe the Nouveau drivers would work better, but >> that isnt to say one doesnt exist. >> >> -Zeke >> >> On 08/22/2014 03:23 PM, r...@nmr.mgh.harvard.edu wrote: >>> >>> Hi, >>> >>> Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to >>> use >>> the "noveau" drivers that come with CentOS 6.5 or would it be better to >>> go >>> with the proprietary drivers from NVIDIA? >>> >>> I would imagine that since FS 5.3 does not use GPU for analysis, this >>> is >>> mainly relevant for visualization (freeview etc) requiring 3D rendering >>> of >>> volumes, surfaces, and tractography results simultaneously. >>> >>> In case it matters, Dell Precision T7500 + NVIDIA Quadra FX 5800 here. >>> >>> Thanks! >>> >>> Tommi >>> >>> --- >>> Tommi Raij, MD, PhD >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] preproc-sess registration problem
Hi Doug, We have an old EPI data set where automatic (preproc-sess) or bbregister with any init type give a bad result. Hence, we are attempting to use a manual register.dat file instead. However, we must be doing something wrong, because changing preproc-sess to use our manual register.dat (done a couple of years ago) seems to have no effect. I suspect our preproc-sess options as not set up correctly. Our goal is to present the results on fsaverage surface. Our preproc-sess command line is as follows: preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session -sliceorder siemens -force -fsd bold -noreg -regfile bold/register.dat The whole analysis script is at /space/adapt/1/users/tapsya/project_AVISI_avml07/avml07/Analysis_avml07_fsaverage.csh FS version = 5.1 machine = adapt (analysis running on cluster) setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs/ individual subject = avml07 surface analysis lhrh, results to be presented on fsaverage surface Total of 3 runs per analysis (each with different number of TRs) Total of categories in mkanalysis-sess = 18 (9 main plus 9 rare target) FIR analysis Thank you for the advice in advance! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] preproc-sess registration problem
Hi Doug, You are absolutely right - I should have noticed the T1 warning in the bbregister logs. I guess funny things can happen when scanning with a short (1.15 sec) TR without fat suppression (also this was Trio before the Tim upgrade and multichannel arrays). We tried bbregister with t1 weighting and indeed it works much better. However, to change only parameter at a time, we would prefer to run the version 5.1 analysis using the old manual register.dat. The next question is how do we do that exactly. As you suggest, we will (inside the bold directory, not inside the individual run directories) cp register.dat register.dof6.dat ... but then how should our preproc-sess command look like in order to avoid re-registering the data and overwriting our registration file? Would this simply be a matter of adding -noreg, such as: preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session -sliceorder siemens -force -fsd bold -noreg -Tommi > wow, that's interesting. Your data is actually T1 weighted! There are a > couple of things you can do. First, you can copy your register.dat over > the register.dof6.dat. An alternative is to run register-sess > (bbregister) with t1 weighting. You can do this by creating a file with > the line "--t1" in it (no quotes) and passing that file to register-sess > with "-bbr-xopts yourfile". > > doug > > r...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> We have an old EPI data set where automatic (preproc-sess) or bbregister >> with any init type give a bad result. Hence, we are attempting to use a >> manual register.dat file instead. However, we must be doing something >> wrong, because changing preproc-sess to use our manual register.dat >> (done >> a couple of years ago) seems to have no effect. I suspect our >> preproc-sess >> options as not set up correctly. Our goal is to present the results on >> fsaverage surface. >> >> Our preproc-sess command line is as follows: >> >> preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session >> -sliceorder siemens -force -fsd bold -noreg -regfile bold/register.dat >> >> The whole analysis script is at >> >> /space/adapt/1/users/tapsya/project_AVISI_avml07/avml07/Analysis_avml07_fsaverage.csh >> >> FS version = 5.1 >> machine = adapt (analysis running on cluster) >> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs/ >> individual subject = avml07 >> surface analysis lhrh, results to be presented on fsaverage surface >> Total of 3 runs per analysis (each with different number of TRs) >> Total of categories in mkanalysis-sess = 18 (9 main plus 9 rare target) >> FIR analysis >> >> Thank you for the advice in advance! >> >> Bests, >> >> Tommi >> >> >> --- >> Tommi Raij, MD, PhD >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ Freesurfer mailing list Freesurfer@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] Coordinate transformations from orig/001.mgz to T1.mgz
Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two images: 1. $SUBJECTS_DIR/$SUBJECT/mri/orig/001.mgz (not altered by recon-all) 2. $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz (altered by recon-all) For (1) above, "Volume Index" in tkmedit looks like this: origin (0,0,0) is at right anterior superior corner of the stack with x=A-P y=S-I z=R-L. Max values in tkmedit display were (255,243,191). The acquisition had 192 sagittal slices so the last number makes sense - not sure why the second figure is not 255 (perhaps just a display thing). The orig/001.mgz stack should be exactly the same stack as in the Nexstim NBS image (which is just the plain DICOM), without any resampling or other processing, just the axes have been reshuffled a bit. For (2) above, "Volume Index" in tkmedit looks like this: origin (0,0,0) is at right posterior superior corner of the stack with x=R-L y=S-I z=P-A. Max values in tkmedit display were (255,255,255). This makes things difficult, as we do not know what exactly recon-all did to orig/001.mgz when it converted it into T1.mgz. Our question is this: Is there a deterministic way to go from orig/001.mgz to T1.mgz Volume Index coordinates? It seems that recon-all has at least added sagittal slices to make the T1.mgz stack into a cube (looking at lateral shift between 001.mgz and T1.mgz, I would guess that 32 1-mm slices on both sides (2*32+192=256) were added)... Further, it is not clear if the orig/001.mgz volume has been shifted, rotated, or resampled by recon-all when turning it into T1.mgz. Thank you for the advice! Bests, Tommi & Aapo ___ Freesurfer mailing list Freesurfer@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] mri_surfcluster .w input from MEG/EEG data
Hi Doug and Matti, I am using mri_surfcluster to threshold and extract ROIs from MEG/EEG source analysis data. The same code used to work fine in Jan 2009, but now I am running into unexpected errors. I wonder if something happened along the way of FreeSurfer and/or MNE stream upgrades and now mne_analyze .w files and mri_surfcluster no longer talk to each other. I first run the usual MEG/EEG analysis using the MNE stream and then save the resulting dSPM map on the surface of the subject as a .w file (using the mne_analyze GUI). For sanity check, I download the overlay in tksurfer and observe that it looks fine (which makes me think that the problem originates at the mri_surfcluster side rather than at mne_analyze; however, see below for evidence suggesting the opposite). on machine adapt nmr-std-env (=FreeSurfer 5.1) mne_setup cd /cluster/scratch/monday/raij/MEEG setenv SUBJECTS_DIR /cluster/scratch/monday/raij/MRIs/ setenv SUBJECT Wyss_000 mri_surfcluster \ --subject Wyss_000 \ --hemi lh \ --in AVL_GA_List1-00150.0-lh.w \ --frame 0 \ --thmin 2 \ --thsign abs \ --minarea 100 \ --olab test01 \ thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ hemi = lh srcid = AVL_GA_List1-00150.0-lh.w srcsubjid = Wyss_000 srcsurf= white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr= -1 minarea= 100 xfmfile= talairach.xfm nth = -1 subjectsdir= /cluster/scratch/monday/raij/MRIs/ FixMNI = 1 - XFM matrix (RAS2RAS) --- /cluster/scratch/monday/raij/MRIs//Wyss_000/mri/transforms/talairach.xfm 0.973 -0.031 -0.031 0.033; 0.001 0.989 0.327 -34.515; 0.008 -0.285 1.073 -30.192; 0.000 0.000 0.000 1.000; Reading source surface /cluster/scratch/monday/raij/MRIs//Wyss_000/surf/lh.white Done reading source surface Computing metric properties Loading source values mri_read(): couldn't determine type of file /autofs/cluster/scratch/monday/raij/MEEG/AVL_GA_List1-00150.0-lh.w ERROR: could not read AVL_GA_List1-00150.0-lh.w as type If I try to convert .w to .mgz I get the error mri_convert AVL_GA_List1-00150.0-lh.w AVL_GA_List1-00150.0-lh.mgz file not found or unknown file type for file AVL_GA_List1-00150.0-lh.w (which makes me think that perhaps the .w file from mne_analyze is incompatible with much of FreeSurfer 5.1 code) Any suggestions? As always, thank you for the advice in advance! Best regards, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_surfcluster .w input from MEG/EEG data
Hi Doug, I am still receiving a similar error. mri_surf2surf inputes the w file and writes out a mgz file and exits apparently ok. However, mri_volcluster still exits with "could not read test-lh.mgz as type" Details: mri_surf2surf \ --srcsubject Wyss_000 \ --trgsubject Wyss_000 \ --hemi lh \ --srcsurfval AVL_GA_List1-00150.0-lh.w \ --trgsurfval test.lh.mgz \ --sfmt w \ --tfmt mgz \ srcsubject = Wyss_000 srcval = AVL_GA_List1-00150.0-lh.w srctype= w trgsubject = Wyss_000 trgval = test.lh.mgz trgtype= mgz srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /cluster/scratch/monday/raij/MRIs/Wyss_000/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to test.lh.mgz mri_surfcluster --subject Wyss_000 --hemi lh --in test-lh.mgz --frame 0 --thmin 2 --thsign abs --minarea 100 --olab test01 thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ hemi = lh srcid = test-lh.mgz srcsubjid = Wyss_000 srcsurf= white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr= -1 minarea= 100 xfmfile= talairach.xfm nth = -1 subjectsdir= /cluster/scratch/monday/raij/MRIs FixMNI = 1 - XFM matrix (RAS2RAS) --- /cluster/scratch/monday/raij/MRIs/Wyss_000/mri/transforms/talairach.xfm 0.973 -0.031 -0.031 0.033; 0.001 0.989 0.327 -34.515; 0.008 -0.285 1.073 -30.192; 0.000 0.000 0.000 1.000; Reading source surface /cluster/scratch/monday/raij/MRIs/Wyss_000/surf/lh.white Done reading source surface Computing metric properties Loading source values mghRead(/autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz, -1): could not open file ERROR: could not read test-lh.mgz as type -Tommi > Hi Tommi, convert the w file to an mgz with mri_surf2surf. Specify the > source format with --sfmt w > doug > > r...@nmr.mgh.harvard.edu wrote: >> Hi Doug and Matti, >> >> I am using mri_surfcluster to threshold and extract ROIs from MEG/EEG >> source analysis data. The same code used to work fine in Jan 2009, but >> now >> I am running into unexpected errors. I wonder if something happened >> along >> the way of FreeSurfer and/or MNE stream upgrades and now mne_analyze .w >> files and mri_surfcluster no longer talk to each other. >> >> I first run the usual MEG/EEG analysis using the MNE stream and then >> save >> the resulting dSPM map on the surface of the subject as a .w file (using >> the mne_analyze GUI). For sanity check, I download the overlay in >> tksurfer >> and observe that it looks fine (which makes me think that the problem >> originates at the mri_surfcluster side rather than at mne_analyze; >> however, see below for evidence suggesting the opposite). >> >> on machine adapt >> nmr-std-env (=FreeSurfer 5.1) >> mne_setup >> cd /cluster/scratch/monday/raij/MEEG >> setenv SUBJECTS_DIR /cluster/scratch/monday/raij/MRIs/ >> setenv SUBJECT Wyss_000 >> >> mri_surfcluster \ >> --subject Wyss_000 \ >> --hemi lh \ >> --in AVL_GA_List1-00150.0-lh.w \ >> --frame 0 \ >> --thmin 2 \ >> --thsign abs \ >> --minarea 100 \ >> --olab test01 \ >> >> thsign = abs, id = 0 >> version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp >> $ >> hemi = lh >> srcid = AVL_GA_List1-00150.0-lh.w >> srcsubjid = Wyss_000 >> srcsurf= white >> srcframe = 0 >> thsign = abs >> thmin = 2 >> thmax = -1 >> fdr= -1 >> minarea= 100 >> xfmfile= talairach.xfm >> nth = -1 >> subjectsdir= /cluster/scratch/monday/raij/MRIs/ >> FixMNI = 1 >> - XFM matrix (RAS2RAS) --- >> /cluster/scratch/monday/raij/MRIs//Wyss_000/mri/transforms/talairach.xfm >> 0.973 -0.031 -0.031 0.033; >> 0.001 0.989 0.327 -34.515; >> 0.008 -0.285 1.073 -30.192; >> 0.000 0.000 0.000 1.000; >> >> Reading source surface >> /cluster/scratch/monday/raij/MRIs//Wyss_000/surf/lh.white >> Done reading source surface >> Computing metric properties >> Loading source values >> mri_read(): couldn't determine type of file >> /autofs/cluster/scratch/monday/raij/MEEG/AVL_GA_List1-00150.0-lh.w >> ERROR: could not read AVL_GA_Lis
Re: [Freesurfer] mri_surfcluster .w input from MEG/EEG data
Oops - my bad, on this last round I mixed one filename dash with a dot. Works now - so (just to remind myself) the new feature is to use mri_surf2surf to convert from w to mgz before running mri_surfcluster. Thanks Doug! :) -Tommi > It looks like that file does not exist: > ls /autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz > ls: /autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz: No such file > or directory > > > r...@nmr.mgh.harvard.edu wrote: >> Hi Doug, >> >> I am still receiving a similar error. mri_surf2surf inputes the w file >> and writes out a mgz file and exits apparently ok. However, >> mri_volcluster >> still exits with >> "could not read test-lh.mgz as type" >> >> Details: >> >> mri_surf2surf \ >> --srcsubject Wyss_000 \ >> --trgsubject Wyss_000 \ >> --hemi lh \ >> --srcsurfval AVL_GA_List1-00150.0-lh.w \ >> --trgsurfval test.lh.mgz \ >> --sfmt w \ >> --tfmt mgz \ >> >> srcsubject = Wyss_000 >> srcval = AVL_GA_List1-00150.0-lh.w >> srctype= w >> trgsubject = Wyss_000 >> trgval = test.lh.mgz >> trgtype= mgz >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> srchemi= lh >> trghemi= lh >> frame = 0 >> fwhm-in= 0 >> fwhm-out = 0 >> label-src = (null) >> label-trg = (null) >> OKToRevFaceOrder = 1 >> Reading source surface reg >> /cluster/scratch/monday/raij/MRIs/Wyss_000/surf/lh.sphere.reg >> Loading source data >> INFO: trgsubject = srcsubject >> Saving target data >> Saving to test.lh.mgz >> >> >> mri_surfcluster --subject Wyss_000 --hemi lh --in test-lh.mgz --frame 0 >> --thmin 2 --thsign abs --minarea 100 --olab test01 >> thsign = abs, id = 0 >> version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp >> $ >> hemi = lh >> srcid = test-lh.mgz >> srcsubjid = Wyss_000 >> srcsurf= white >> srcframe = 0 >> thsign = abs >> thmin = 2 >> thmax = -1 >> fdr= -1 >> minarea= 100 >> xfmfile= talairach.xfm >> nth = -1 >> subjectsdir= /cluster/scratch/monday/raij/MRIs >> FixMNI = 1 >> - XFM matrix (RAS2RAS) --- >> /cluster/scratch/monday/raij/MRIs/Wyss_000/mri/transforms/talairach.xfm >> 0.973 -0.031 -0.031 0.033; >> 0.001 0.989 0.327 -34.515; >> 0.008 -0.285 1.073 -30.192; >> 0.000 0.000 0.000 1.000; >> >> Reading source surface >> /cluster/scratch/monday/raij/MRIs/Wyss_000/surf/lh.white >> Done reading source surface >> Computing metric properties >> Loading source values >> mghRead(/autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz, -1): could >> not open file >> ERROR: could not read test-lh.mgz as type >> >> -Tommi >> >> >> >>> Hi Tommi, convert the w file to an mgz with mri_surf2surf. Specify the >>> source format with --sfmt w >>> doug >>> >>> r...@nmr.mgh.harvard.edu wrote: >>> >>>> Hi Doug and Matti, >>>> >>>> I am using mri_surfcluster to threshold and extract ROIs from MEG/EEG >>>> source analysis data. The same code used to work fine in Jan 2009, but >>>> now >>>> I am running into unexpected errors. I wonder if something happened >>>> along >>>> the way of FreeSurfer and/or MNE stream upgrades and now mne_analyze >>>> .w >>>> files and mri_surfcluster no longer talk to each other. >>>> >>>> I first run the usual MEG/EEG analysis using the MNE stream and then >>>> save >>>> the resulting dSPM map on the surface of the subject as a .w file >>>> (using >>>> the mne_analyze GUI). For sanity check, I download the overlay in >>>> tksurfer >>>> and observe that it looks fine (which makes me think that the problem >>>> originates at the mri_surfcluster side rather than at mne_analyze; >>>> however, see below for evidence suggesting the opposite). >>>> >>>> on machine adapt >>>> nmr-std-env (=FreeSurfer 5.1) >>>> mne_setup >>>> cd /cluster/scratch/monday/raij/MEEG >>>> setenv SUBJECTS_DIR /cluster/scratch/monday/raij/MRIs/ >>>> setenv SUBJECT Wyss_000 >>>> >>>> mri_surfcluster \ >>>> --subject Wyss_000 \ >&
[Freesurfer] RA position at the Martinos Center
We are seeking an RA for a data analysis oriented position. Previous experience with FreeSurfer FS-FAST and MEG/EEG MNE analysis stream is highly valued. Ability to use MATLAB for mathematical modeling of fMRI and MEG/EEG data is required. For details, please see http://www.nmr.mgh.harvard.edu/martinos/opportunities/employment.php#rs032609 Tommi Raij r...@nmr.mgh.harvard.edu --- Tommi Raij, M.D., Ph.D. TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] opseq2 efficiency vs VRF
Hi Doug and other Freesurfers, We are trying to balance the power of different event-related fMRI runs (each consisting of a different experimental condition with different interstimulus intervals) using the optseq2 definition for efficiency. Our outcome metric is the BOLD % signal change amplitude - we expect different runs to show different amplitudes. We use a FIR model. Because of the variable under investigation (interstimulus interval) we must have different number of stimuli in each run. We are uncertain as to which optseq2 efficiency measure more accurately suits this situation. I know you typically prefer "VRF" over "Efficiency". However, is VRF better suited for reflecting the power of statistical contrast (for example for t-test and F-values) as opposed to "raw" BOLD % signal change? In other words, would "Efficiency" more accurately reflect the balance for just the BOLD % signal change? The ultimate goal is to make sure that changes in BOLD % signal change amplitude are not due to the different number of stimuli across runs. Thanks! Best regards, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] FS-FAST seq.info with multiple ntrs
Hi Doug, I have 3 functional runs that have a different number of TRs (from all subjects). The design is rapid event-related and the different runs are matched for statistical power despite that the number of trs is different for each run. I would like to contrast the runs with different ntrs as a first level analysis (within subjects to begin with). However there is only one seq.info file (that contains the ntrs value). Hence selxavg-sess fails if I try to analyze the runs at the same time. The Freesurfer wiki says that runs should have the same ntrs, but this is not possible in this case. Is there a way around this problem? For example, if selxavg-sess is the only step that reads the ntrs value, can I just change the contents of the seq.info file and do the selxavg-sess step for the runs separately? Or do other analysis steps also need a correct ntrs value? Also can I tell selxavg-sess to look for a custom filename instead of seq.info? This might make things more flexible. Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] func2sph-sess target brain setting
Hi, Backround: I am running a fixed effects group analysis with fsaverage (mne305) as the target brain, and merging the activations across subjects on the spherical surface. The individual functional sessions have been co-registered to the individuals' structural brain reconstruction (i.e. the register.dat file inside the bold directory links the functional and structural data within subjects only). Problem: I am not sure how to set the group analysis func2sph-sess and paint-sess "target brain" parameters correctly. Version and environment: I am using the current Martinos Center FreeSurfer standard installation (vs. >3) under nmr-std-env and all the structural reconstructions are new as well. Outline of the analysis (list of commands): preprocessing mkanalysis-sess.new selxavg-sess mkcontrast-sess stxgrinder-sess func2sph-sess <- sphsmooth-sess isxavg-fe-sess stxgrinder-sess paint-sess <- Specific question (with possible answers): *** 1 *** Should I set the target brain already at func2sph-sess: func2sph-sess -analysis XXX -sf sessid -df sesspar -trgsubject fsaverage (if the -trgsubject setting is omitted, then the target appears be the default = ico order 7) *** 2 *** Or is it sufficient (if I ignore the -trgsubject parameter above) to set: paint-sess -analysis XXX -contrast YYY -subject fsaverage -space sph -isxavg fixed -s fegroup -df group.sesspar (here fegroup = the folder where the fixed effects analysis is stored, set at isxavg-fe-sess -s fegroup) *** 3 *** Or must/should I do both 1 and 2 of the above. I am using surf-sess/tksurfer to view the results and set -subject fsaverage even there. I get results that look reasonable either way. I just wonder what is the difference between the methods, and if either method is unambiguously correct. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer hemodynamic waveforms for group analysis
Dear Fellow Freesurfers, I am trying to display HDR waveforms (time courses) for group level FIR analyses in tksurfer. When opening the group analysis data with tkmedit and a functional overlay, obviously some sort of time course data is loaded, because I can scroll back and forth between the different time points/frames of the functional overlay (for the specific contrast that I loaded). However the load timecourse function does not seem to be working. When attempting to load a hemodynamic waveform, I receive either an error (func_load_timecourse: error in FunD_New) without opening the HDR window, or then the time course volume is "interpreted as encoded scalar volume" and only one time point, of only one contrast, is shown in the HDR window. I have tried downloading all possible and impossible files related to the group analysis (.hdr/.bhdr/.bfloat/.dat/.mat/.w) from both within the specific contrast directory or the one higher level, but they all fail in either of the two ways above. The wiki, in this case, was not very helpful in trying to discover which file to load: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization Is this function currently functional? If so, which file should I load? Details: group brain = fsaverage STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/ SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/ environment = nmr-std-env on machine ai (FreeSurfer vs >3) group analysis name = fegroup, analysis = ISI1TR_BERT_ERFIRsm5pf5tpefsub example contrast: AV-REST Thanks for your help! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] func2sph-sess target brain setting
Thanks Doug, just a quick check that I understood correctly: > > There are two issues here: > > 1. Make sure that all of your subjects have been reconstructed with > the same version of freesurfer (it looks like you have done this). Correct > 2. If you've used an "older" version of freesurfer for the recon, then > render (ie, paint) your results on average7 (the default). If > you've used a "newer" version (which you have), then render them on > fsaverage. Does this mean that setting "func2sph-sess -trgsubject fsaverage" makes no difference in this case (as long as fsaverage is defined in paint-sess)? -T > doug > > > > > On Wed, 7 Jun 2006 [EMAIL PROTECTED] wrote: > >> Hi, >> >> Backround: I am running a fixed effects group analysis with fsaverage >> (mne305) as the target brain, and merging the activations across >> subjects >> on the spherical surface. The individual functional sessions have been >> co-registered to the individuals' structural brain reconstruction (i.e. >> the register.dat file inside the bold directory links the functional and >> structural data within subjects only). >> >> Problem: I am not sure how to set the group analysis func2sph-sess and >> paint-sess "target brain" parameters correctly. >> >> Version and environment: I am using the current Martinos Center >> FreeSurfer >> standard installation (vs. >3) under nmr-std-env and all the structural >> reconstructions are new as well. >> >> Outline of the analysis (list of commands): >> >> preprocessing >> mkanalysis-sess.new >> selxavg-sess >> mkcontrast-sess >> stxgrinder-sess >> func2sph-sess <- >> sphsmooth-sess >> isxavg-fe-sess >> stxgrinder-sess >> paint-sess <- >> >> Specific question (with possible answers): >> >> *** 1 *** Should I set the target brain already at func2sph-sess: >> func2sph-sess -analysis XXX -sf sessid -df sesspar -trgsubject >> fsaverage >> (if the -trgsubject setting is omitted, then the target appears be the >> default = ico order 7) >> >> >> *** 2 *** Or is it sufficient (if I ignore the -trgsubject parameter >> above) to set: >> paint-sess -analysis XXX -contrast YYY -subject fsaverage -space sph >> -isxavg fixed -s fegroup -df group.sesspar >> (here fegroup = the folder where the fixed effects analysis is stored, >> set >> at isxavg-fe-sess -s fegroup) >> >> >> *** 3 *** Or must/should I do both 1 and 2 of the above. >> >> >> I am using surf-sess/tksurfer to view the results and set -subject >> fsaverage even there. >> >> I get results that look reasonable either way. I just wonder what is the >> difference between the methods, and if either method is unambiguously >> correct. >> >> Thanks, >> >> Tommi >> >> --- >> Tommi Raij, M.D., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST: mkcontrast-sess -setwdelay
Hi, I have a large (~100) number of FIR analyses where I need to set the weights for each post-stimulus delay (and then collapse them with -sumdelays). The weights are the same for all analyses. However the -setwdelay weights can only be entered manually upon prompt. This means that I would have to sit by the computer for a few days just to copy-paste a short series of numbers every 25 min. This makes no sense of course. Is there a way to make feeding the -setwdelay numbers part of the analysis script so I could just let it run without human intervention? I would be very happy if I could just set in the analysis script, for example, mkcontrast-sess -analysis XXX -setwdelay 0 0 0 0 1 1 1 0 0 0 0 0 -sumdelays -contrast A-REST -a 1 -c 0 Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] viewing group analysis results in tkmedit (3D) while using spherical space intersubject morphing
Hi FreeSurfers, A small group analysis question of fMRI data (fixed effects). The target brain is "fsaverage". I have resampled and averaged the stat maps across subjects in _spherical_ space using func2sph-sess / sphsmooth-sess / isxavg-fe-sess / stxgrinder-sess. Viewing the results on a "fsaverage" surface with tksurfer works fine, thanks. Now I would like to also view the mean functional maps in 3D space (tkmedit) on the "fsaverage" brain. This does not seem to work - obviously because the results were calculated in spherical space and were never resampled back to 3D space. Is there a way to resample the group average from sperical space to 3D space so that it could be viewed in tkmedit? Or is the only way to achieve something like this to recalculate the analyses entirely in Talairach space without using the spherical space? To make the results actually comparable between 3D (tkmedit) and surface-based (tksurfer) viewing, I think I should use the same type of space for intersubject averaging - preferably spherical in both cases. Hence, if a tool such as sph2func-sess exists (could not find it in the wiki), or there is a workaround, any suggestions would be very much welcome. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST group analysis paint question
Hi, I would like to paint group analysis results to the surface of the fsaverage brain to produce .w files. With individual subject analyses (that were calculated in individual space, i.e. not morphed), I have been able to use mri_vol2surf in this manner: mri_vol2surf --src V-REST/sig --src_type bfloat -srcreg ../register.dat --hemi lh --o ./V-REST-lh.w --out_type paint In the group analysis, the individual subjects' volumes were morphed into sperical space where the spatial alignment across subjects was done. I used the average brain "fsaverage" as the target brain. Here the above mri_vol2surf will not work. I am unsure how to do the corresponding paint job for the morphed group analysis data. Would the following command do what needs to be done? mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage --srcsurfval V-REST/sig-lh --src_type bfloat --hemi lh --trgsurfval ./V-REST-lh.w --trg_type paint Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS-FAST group analysis paint question
... but if I need to create the .w files as output, then using the mri_surf2surf is the way to go, right? -Tommi > > You actually should not need to do any transformation, just render the > sig map directly in tksurfer, ie, > > tksurfer fsaverage lh inflated -overlay sig-lh.bhdr > > fsaverage is the sphere (7th order icosahedron). > > > > [EMAIL PROTECTED] wrote: > >>Hi, >> >>I would like to paint group analysis results to the surface of the >>fsaverage brain to produce .w files. >> >>With individual subject analyses (that were calculated in individual >>space, i.e. not morphed), I have been able to use mri_vol2surf in this >>manner: >> >>mri_vol2surf --src V-REST/sig --src_type bfloat -srcreg ../register.dat >>--hemi lh --o ./V-REST-lh.w --out_type paint >> >>In the group analysis, the individual subjects' volumes were morphed into >>sperical space where the spatial alignment across subjects was done. I >>used the average brain "fsaverage" as the target brain. Here the above >>mri_vol2surf will not work. >> >>I am unsure how to do the corresponding paint job for the morphed group >>analysis data. Would the following command do what needs to be done? >> >>mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage --srcsurfval >>V-REST/sig-lh --src_type bfloat --hemi lh --trgsurfval ./V-REST-lh.w >>--trg_type paint >> >>Thanks, >> >>Tommi >> >>--- >>Tommi Raij, M.D., Ph.D. >>MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >>Bldg 149, 13th St >>Charlestown, MA 02129 >>U.S.A. >> >>[EMAIL PROTECTED] >>___ >>Freesurfer mailing list >>Freesurfer@nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer time course script help
Dear Freesurfers,
We are trying to write a tksurfer tcl script that would save FIR analysis
hemodynamic waveform time course windows in postscript format (rgb or tiff
are not sufficient as we need to do a lot of editing on the figures with
Adobe Illustrator to get publishable figures. No, not THAT kind of editing
:)). The script loads a label, loads a hemodynamic waveform, calculates
the mean value across the label, and plots the curves. Most of the stuff
is working already, thanks to Kevin Teich, but a few pieces are missing.
The functions we are looking for exist in the GUI, but we could not find
the corresponding script commands in the wiki or archive. Could you tell
us the tcl script commands for:
1. Save the time course window in //.ps
2. Select only some of the contrasts for display (e.g., we have contrasts
0-7 and only want to display 1, 2, and 3)
3. Setting "subtract pre-stim average" on, i.e. forcing the pre-stimulus
time window mean values to zero on the y-axis ("baseline correction").
I will add the script to the wiki when we have it working. Very convenient
when you have multiple contrasts in multiple experimental conditions and
many ROIs in many subjects - just edit the list of ROIs/labels and time
courses to be loaded, and let the computer do the rest!
Thanks!
Tommi
---
Tommi Raij, M.D., Ph.D.
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th St
Charlestown, MA 02129
U.S.A.
[EMAIL PROTECTED]
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[Freesurfer] Rendering results of custom fMRI analyses on FreeSurfer surface
Dear FreeSurfers, We are running a FS-FAST group analysis where the individual subjects are morphed to an average brain via spherical surface. The output of that analysis (sig statistical maps, left hemisphere) is saved in $STUDY_DIR//boldsig-lh_XXX.bfloat, Question 1: In the above, XXX is usually the slice number. However we have 25 slices in the input data, and our folder contains only bfloat numbers 000-006. I guess morphing the individual data to a sperical surface for group analysis changes the original slice structure, and hence the numbering. I guess we have seven "slices" because in the command func2sph-sess we defined -icoorder 7 (icosahedron order). Correct? Question 2: We use the above sig-lh_XXX.bfloat files as input to a custom matlab analysis. Remember we have XXX=000-006. What should the output of the matlab analysis look like so that rendering it onto a FreeSurfer surface will work? Is there any documentation related to this? Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Percent signal change: what stats to read
Hi, We have calculated a FIR group analysis with FS-FAST and have the corresponding ces, cesvar, f, fsig, iminsig, minsig, sig, and t maps in the contrast folders. Which one of these should I use for presenting % signal change? We want to do some further analyses of the group analysis results with matlab and would need to use % signal change as the input values for those analyses. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer BOLD time course display: show multiple overlays?
Hi Surfers, To facilitate comparison of ROI BOLD waveforms across different experiments we are trying to find a way to plot time courses of *** multiple overlays *** simultaneously in the tksurfer time course window. Is there a way to do this using the tcl script? Usually the time course window shows the multiple contrasts for a single overlay, but as soon as I change the overlay, the old time courses are erased and the time courses change to the new overlay. I guess what I am saying is that we would like to avoid erasing the old stuff in the time course window and just keep adding more waveforms from new overlays (with the possibility of still selecting which waveforms will be visible). We are trying to do this within tksurfer. Any suggestions are much appreciated! Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer BOLD time course display: show multiple overlays?
Ok Doug, I guess I should have talked about time courses instead of
overlays. Let me clarify:
on machine stim (via remote VNC):
nmr-dev-env
cd /space/cuzco/7/user/raij/avml_fmri_mctogether
setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri
setenv SUBJECT fsaverage
Launch tksurfer:
tksurfer fsaverage lh inflated
Load first set of time courses from the first experiment ("ISI1TR") using
the tcl shell:
func_load_timecourse
fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/h-lh.bhdr 3
Now, as expected, when I click on the brain, I will see 6 waveforms, one
for each contrast ("Condition") for the vertex point I selected. (Actually
I load a ROI from the tcl shell and set the waveform display to show the
mean value within the ROI, but this should not make any difference to the
current question.)
Now for the interesting part. I want to overlay more waveforms from
another experiment ("ISI2TR") usingthe tcl shell for the same vertex point
(or ROI):
func_load_timecourse
fegroup/bold/group_ISI2TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/h-lh.bhdr 3
However, instead of getting 6 more waveforms to add to a total of 12
waveforms, the earlier 6 waveforms disappear and I get only the new 6
waveforms.
The question is, how do I get to keep all 12 waveforms on the display?
(Eventually I will even want to load a third experiment to get 6 more
waveforms, and finally, switch off all other waveforms except Condition 3
in each of the three experiments, but once the above problem is sorted out
then I think I can manage the rest - we already have working tcl scripts
for the rest of this).
Thanks,
Tommi
> Not sure what you mean. tksurfer/tkmedit do not plot overlays, per se.
> Rather, you pass a timecourse file to it, and is plots the values in the
> time course file.
>
> [EMAIL PROTECTED] wrote:
>
>>Hi Surfers,
>>
>>To facilitate comparison of ROI BOLD waveforms across different
>>experiments we are trying to find a way to plot time courses of ***
>>multiple overlays *** simultaneously in the tksurfer time course window.
>>
>>Is there a way to do this using the tcl script? Usually the time course
>>window shows the multiple contrasts for a single overlay, but as soon as
>> I
>>change the overlay, the old time courses are erased and the time courses
>>change to the new overlay. I guess what I am saying is that we would like
>>to avoid erasing the old stuff in the time course window and just keep
>>adding more waveforms from new overlays (with the possibility of still
>>selecting which waveforms will be visible).
>>
>>We are trying to do this within tksurfer.
>>
>>Any suggestions are much appreciated!
>>
>>Thanks,
>>
>>Tommi
>>
>>---
>>Tommi Raij, M.D., Ph.D.
>>MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
>>Bldg 149, 13th St
>>Charlestown, MA 02129
>>USA
>>___
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>
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[Freesurfer] func2sph-sess registration question - where should individual subject's register.dat files be?
Hi, I did not see this documented anywhere so I figured it would be best to double check. Any group analysis relies on that the individual functional and structural data have first been aligned, and there is therefore a register.dat file in the individual subject's directory. This is usually saved at $STUDY_DIR/$SESSION_DIR/bold/register.dat Now, when I run a group analysis, the functional (or structural) space of each individual subject is re-mapped onto the structural space of the target brain. This process must have access to the correct subject-specific register.dat files for each individual subject. In the case of a spherical surface group analysis, I would do this re-mapping by func2sph-sess that I run inside the $STUDY_DIR. The command would have the format func2sph-sess -analysis -sf sessid -df sesspar -trgsubject fsaverage -projfrac 0.3 where the contents of the "sessid" file would list all my $SESSION_DIRs (i.e., different subjects). Question: Where does func2sph-sess look for the individual level register.dat files? I assume it will automatically find them at $STUDY_DIR/$SESSION_DIR/bold/register.dat Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST: FIR analysis baseline corrected BOLD % signal change values?
Hi, We are measuring BOLD % signal change levels (from cespct maps) across separate analyses and the issue of whether the cespct values are pre-stimulus baseline corrected - or not - obviously would be expected to effect the results. We use a FIR group analysis of a rapid event-related design with a - mkanalysis-sess -prestim = 2 TRs - mkcontrast-sess -rmprestim We then use a tcl script to plot the numerical values in a table - here we use set gbPreStimOffset 1 func_print_timecourse_selection $lpath/.txt Visually, when we use tksurfer to view the time course results from the bold//h-lh.bhdr file, then all contrasts included in the analysis are showed at the same time (nice) and the two prestimulus values are included in the display. So far so good. However there is no option to view the results as BOLD % signal change (cespct). A minor annoyance is that the time courses are not baseline corrected despite that we used the -rmprestim option as explained above (they change to be baseline corrected only after we push the View/Configure/Time Course putton Remove prestim). The only way we have found to visually view (or plot with the tcl script) the cespct values is to look at the time course results inside the folders for specific contrasts (e.g., bold//A-REST/cespct-lh.bhdr). However here we never see any prestimulus values (otherwise the same full analysis time window as above is shown), so we do not know if the mean of the two prestim points has been subtracted from the amplitudes (= baseline correction). Below please find the detailed commands for looking at the h-lh.bhdr and cespct curves. We would appreciate any advice how to get the pre-stim values visible even for cespct and/or double check that the cespct values (when plotted using the tcl script) are baseline corrected. Thanks!!! -Tommi Details: On machine cuzco nmr-dev-env (or nmr-std-env, does not seem to make a difference in this case) cd /space/cuzco/7/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Load the h-lh.bhdr curves (prestim baseline are visible, no cespct option): tksurfer fsaverage lh inflated -timecourse fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/h-lh.bhdr Load the cespct-lh.bhdr curves, no prestim baseline data points visible: tksurfer fsaverage lh inflated -timecourse fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/A-REST/cespct-lh.bhdr --- Tommi Raij, MD., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST: problem with extracting BOLD time courses with a tksurfer tcl script
Hi, I am trying to extract numerical values for BOLD time courses of (a large number of) ROIs. For this purpose I use a tksurfer tcl script. Everything works fine when I only have a small number (~6) of contrasts/stimulus categories (as defined in the paradigm files), but if I increase the number of stimulus categories to 14-18, the script dies without producing anything. I am able to produce the numerical tables semi-manually with the GUI/tcl shell even for the large number of stimulus categories so I do not quite figure what gives. However, doing this manually for all our data would be impossible. Any suggestions how I could circumvent this problem? (The visualization part in the script below, that draws the actual time course display, is not necessary for producing the numerical tables, but removing that part of the script does not help - it still dies.) Any suggestions much appreciated! Also if anyone needs the full script I am happy to send you a copy - however notice that currently one of the command lines only works in the developmental environment (nmr-dev-env). Cheers, Tommi Specs: on machine ai nmr-dev-env cd /space/cuzco/12/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage #Here is the part of the subroutine that does the extraction (to run the whole thing from the master script that sets the variable values, launch run-label-FIR-h.csh in the same directory): # Set curvature for lh set curv lh.curv read_binary_curv set curvflag 1 # Clear earlier labels labl_remove_all # Clear earlier timecourses func_clear_selection # Load new label (use actual path to label file instead of $lname if running the script by itself) labl_load $lpath/$lname.label # Load new timecourse. 3 = No registration needed. # (use actual path to time course file [e.g., bold//h-lh.bhdr] instead of $timecourse if running the script by itself) func_load_timecourse $timecourse 3 # Set timecourse to show average value across all vertices included in the label set gaLinkedVars(func_graph_avg_mode) 2 # Some draw command, dunno what it does really SendLinkedVarGroup graph # Select only some of the contrasts for display. Specifically, here turn off contrasts 4-6 # General format: set gGraphSetting(,visible) <0|1> # where is: Red/Green/Blue/Purple/Brown/Pink/Gray/LightBlue/Yellow/Orange # "Red" is condition zero (NULL), "Green" is condition one, etc. set gGraphSetting(Brown,visible) 0 set gGraphSetting(Pink,visible) 0 set gGraphSetting(Gray,visible) 0 # Adjust amplitude (y-axis, % BOLD signal change) scale from -1 to +2 .wwGraph.gwGraph.gwGraph axis config y -min -1 -max 2 # Pre-stimulus baseline correction (to turn OFF, use 0) set gbPreStimOffset 1 # Draw time course display (this command works only in nmr-DEV-env version!) Graph_SelectVerticesFromMode # Save text file listing the numerical time course values for all categories func_print_timecourse_selection $lpath/$lname-$aname-h.xls # Save time course display as postscript Graph_SaveToPS $lpath/$lname-$aname-h.ps ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Color threshold in freesurfer
What is the corresponding tcl variable called (i.e. the one that selects between the three options Linear/Linear Opaque/Piecewise)? Thanks, Tommi > Kevin has now implemented this in tkmedit in dev. > > doug > > Doug Greve wrote: > >> >> Kevin has just made a change to the default way that the DEV version >> of tksurfer displays colors in overlays. The change has to do with the >> way the color is displayed near the threshold (fthresh). Previously, >> as a superthreshold value approached the threshold, its color and >> opacity would change. The result was that voxels at or just above >> threshold would be transparent, making them look like they were not >> active. The default now is to make them opaque regardless of value (as >> long as they are above threshold). >> >> When you look at the overlay configuation GUI, you will now see three >> items under "Threshold": >> >> Linear >> Linear Opaque >> Piecewise >> >> By default, "Linear Opaque" will be checked. To use the old behavior, >> check "Linear". >> >> Note that you can still control the overall opacity with the slider at >> the top of the GUI. >> >> Kevin is working on changing tkmedit. I'll let you know when that is >> ready. >> >> doug >> >> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer - list overlay values inside a label
Hi Doug & Kevin, I am trying to save a text list from tksurfer that contains all the overlay values (one value per each vertex point) inside in a functionally defined label. The labels were originally defined from a different data set than the overlays where I need the values. The overlay where I want the values picked from is in the format of a series of spherical surface files (ico7): *_time005-tau-lh_000.bfloat *_time005-tau-lh_001.bfloat *_time005-tau-lh_002.bfloat *_time005-tau-lh_003.bfloat *_time005-tau-lh_004.bfloat *_time005-tau-lh_005.bfloat *_time005-tau-lh_006.bfloat Notice that our overlay does not have the usual h-lh.bhdr files that would collect all the time frames and contrast conditions (this is after some custom post-processing) so we have to access the *000.bfloat -> *006.bfloat files directly. Not sure that matters though. Any suggestions how to come about this? I tried to look at the tcl scripting reference but did not quite see what I needed there (or then I just did not understand what I read :). Thanks!!! -Tommi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer - list overlay values inside a label
Ahh - that sounds exactly like what I need! So a script like this would do the trick (Kevin could you please have a quick look): tksurfer fsaverage lh inflated # tcl script sharts here # Load curvature set curv lh.curv read_binary_curv set curvflag 1 # Load my overlay (referring to the first file 000 loads all files 000-006?) sclv_read_from_volume 0 _000.bfloat 3 # Load my label labl_load .label # Output the overlay values for the vertices inside the label write_labeled_vertices .txt Thanks Kevin! -Tommi > If you have an overlay loaded, and you save a label, the label file that > is created will have the current overlay values in the last column. Does > this do what you want? > > > On Wed, 2007-04-18 at 17:01 -0400, [EMAIL PROTECTED] wrote: >> Hi Doug & Kevin, >> >> I am trying to save a text list from tksurfer that contains all the >> overlay values (one value per each vertex point) inside in a >> functionally >> defined label. The labels were originally defined from a different data >> set than the overlays where I need the values. >> >> The overlay where I want the values picked from is in the format of a >> series of spherical surface files (ico7): >> >> *_time005-tau-lh_000.bfloat >> *_time005-tau-lh_001.bfloat >> *_time005-tau-lh_002.bfloat >> *_time005-tau-lh_003.bfloat >> *_time005-tau-lh_004.bfloat >> *_time005-tau-lh_005.bfloat >> *_time005-tau-lh_006.bfloat >> >> Notice that our overlay does not have the usual h-lh.bhdr files that >> would >> collect all the time frames and contrast conditions (this is after some >> custom post-processing) so we have to access the *000.bfloat -> >> *006.bfloat files directly. Not sure that matters though. >> >> Any suggestions how to come about this? I tried to look at the tcl >> scripting reference but did not quite see what I needed there (or then I >> just did not understand what I read :). >> >> Thanks!!! >> >> -Tommi >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Kevin Teich > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer time course window
Hi Elaine, Try this: # Adjust amplitude (y-axis) scale from -1 to +2 .wwGraph.gwGraph.gwGraph axis config y -min -1 -max 2 Either type it in the command window or use it as part of a tcl script. Bests, Tommi > Hello Freesurfer, > > Is there a way to adjust or set the y-axis of the time course window in > tksurfer? > > Thanks in advance, > Elaine > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Q: masking statistical overlays
Dear Fellow Surfers, Is there a FreeSurfer way to mask a stat map overlay, on the inflated cortical surface, in a way that the masked vertex points (a) are transparent in the overlay display (just the underlying dark gray/light gray curvature is showing)? (b) do not effect label-specific HDR time courses (i.e., only unmasked vertex points are taken into account when calculating the HDR curve)? We can edit the stats map with our custom script to generate the mask (e.g., mark all masked vertex points as 0 in the overlay), but it seems that in a stats map every vertex point needs to have an overlay value (i.e., we cannot just skip the vertex points we want to omit - right?). Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Q: masking statistical overlays
Hi Bruce & Surfers, OK, we created a .w file and it looks at is should so part (a) below is solved. However we cannot seem to extract a list of functional overlay values of vertex points included in a label, which was why we needed to do this in the first place. Our goal is to get rid of some bad vertex points points in our functional overlay by creating a mask that excluded them, then load a label, and use labl_save to create a list of overlay values contained within the label (that does not include the vertex points that were masked away). Bruce, Kevin, Doug, any suggestions? Bests, Tommi > Hi Tommi, > > the w-file format is sparse and doesn't have to cover the surface, but > the .mgz does. > > Bruce > > On Tue, 19 Jun 2007 [EMAIL PROTECTED] wrote: > >> Dear Fellow Surfers, >> >> Is there a FreeSurfer way to mask a stat map overlay, on the inflated >> cortical surface, in a way that the masked vertex points >> >> (a) are transparent in the overlay display (just the underlying dark >> gray/light gray curvature is showing)? >> >> (b) do not effect label-specific HDR time courses (i.e., only unmasked >> vertex points are taken into account when calculating the HDR curve)? >> >> We can edit the stats map with our custom script to generate the mask >> (e.g., mark all masked vertex points as 0 in the overlay), but it seems >> that in a stats map every vertex point needs to have an overlay value >> (i.e., we cannot just skip the vertex points we want to omit - right?). >> >> Thanks! >> >> -Tommi >> >> --- >> Tommi Raij, M.D., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Correction: Re: [Freesurfer] Q: masking statistical overlays
Correction: We want to use func_print_timecourse_selection (not labl_save) to output the tables that contain the means across the label (with the bad vertex points excluded by previously done masking). However I think the time course functions are not compatible with the .w file format? Right, Doug? Then, I guess the question is, how do we mask the bad vertex points out of the time course volumes? -Tommi --- Hi Bruce & Surfers, OK, we created a .w file and it looks at is should so part (a) below is solved. However we cannot seem to extract a list of functional overlay values of vertex points included in a label, which was why we needed to do this in the first place. Our goal is to get rid of some bad vertex points points in our functional overlay by creating a mask that excluded them, then load a label, and use labl_save to create a list of overlay values contained within the label (that does not include the vertex points that were masked away). Bruce, Kevin, Doug, any suggestions? Bests, Tommi > Hi Tommi, > > the w-file format is sparse and doesn't have to cover the surface, but the .mgz does. > > Bruce > > On Tue, 19 Jun 2007 [EMAIL PROTECTED] wrote: > >> Dear Fellow Surfers, >> >> Is there a FreeSurfer way to mask a stat map overlay, on the inflated cortical surface, in a way that the masked vertex points >> >> (a) are transparent in the overlay display (just the underlying dark gray/light gray curvature is showing)? >> >> (b) do not effect label-specific HDR time courses (i.e., only unmasked vertex points are taken into account when calculating the HDR curve)? >> >> We can edit the stats map with our custom script to generate the mask (e.g., mark all masked vertex points as 0 in the overlay), but it seems that in a stats map every vertex point needs to have an overlay value (i.e., we cannot just skip the vertex points we want to omit - right?). >> >> Thanks! >> >> -Tommi >> >> --- >> Tommi Raij, M.D., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST: missing time frame & time labeling of FIR analyses
Hi, I have done a FIR analysis of event-related data where my time window is 16 TR:s long, consisting of 2 pre-stimulus time frames plus 14 post-stimulus time frames. I view the results with tksurfer. If I load the results from the h-lh.bhdr file, I have all 16 time frames (0-15) which is as it should be. However, if I load one of the contrast stat maps (e.g., cespct-lh.bhdr) I only have 13 time frames (0-12). I should expect 14 time frames (as the two pre-stimulus time frames are not supposed to show up). I therefore have one time frame missing, and I do not know if my time scale is off by one frame or if the last frame is missing. So, which time frame is it that the cepct-lh.bhdr is missing - the 3rd or the 16th? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Number of voxels that intersect with inflated brain surface
Dear FreeSurfers, Is there a way to estimate the number of fMRI voxels that intersect with the FreeSurfer anatomical inflated surface space? -"- for a given surface label? We need this as N for calculations of statistical significances (to correct for the oversampling of the orginal 3D voxel space by very densely spaced vertex points on the surface). For this purpose, the voxel size was 3.125 x 3.125 x 4.4 mm, the FOV covered the entire brain, and the anatomical brain is "fsaverage". Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer error: Load Time Course causes abort
Hi guys, On machine inv (more or less the same error on machine ai) nmr-dev-env (same error on nmr-std-env) cd /space/cuzco/2/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT fsaverage tksurfer fsaverage lh inflated -overlay avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr -timecourse avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr Output: surfer: current subjects dir: /space/cognito/5/users/raij/subjects_mri/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/cuzco_002/users/raij/avml_fmri_mctogether surfer: Reading header info from /space/cognito/5/users/raij/subjects_mri//fsaverage/mri/T1.mgz reading group avg surface area 822 cm^2 from file surfer: vertices=163842, faces=327680 INFO: bvolumeRead: min = 0, max = 0 *** glibc detected *** corrupted double-linked list: 0x060b7db0 *** Abort Oddly enough, on machine ai, if I leave out the -timecourse part of the command line, the FreeSurfer window opens with the correct overlay and I can scroll through conditions and time points. Further, if I then manually load the timecourse from File/Load Time Course... menu, this works giving the time course display just as it should Even more oddly, on machine inv (which is spanking new and has lots of RAM etc) even the above basic command line with only loading the overlay gives the above glibc error. I have 8 subjects * 66 labels = timecourses of 528 labels to extract, which makes this clearly a script job - the only practical solution would be to find a way to make the command line work. Suggestions? For example, could it be that this has something to do with nvidia drivers? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer error: Load Time Course causes abort
Nick, Thanks for looking into this - we are stalled in our analysis until we find a way around this! The answer to your question is no - I have tried the command in cuzco (via ssh), ai (directly), and inv (directly), and I receive the glibc error on all of them. If you think it would be a good idea to try it on more linux boxes, just let me know. Bests, Tommi > Tommi, > > Do you have a machine on which this script can run without the glibc > error? I have been able to recreate the error you see in a debugger on > inv, but can't figure out what is going wrong. (Doug, the glibc error > occurs when fclose is called on line 565 of mriFunctionalDataAccess.c). > Doug or I will need to look into this further. > > Nick > > On Wed, 2007-09-05 at 19:02 -0400, [EMAIL PROTECTED] wrote: >> Hi guys, >> >> On machine inv (more or less the same error on machine ai) >> nmr-dev-env (same error on nmr-std-env) >> >> cd /space/cuzco/2/users/raij/avml_fmri_mctogether/ >> >> setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ >> setenv SUBJECT fsaverage >> >> tksurfer fsaverage lh inflated -overlay >> avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr >> -timecourse >> avml07_session_BRISI08/bold/group_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sphsm10/h-lh.bhdr >> >> >> Output: >> >> surfer: current subjects dir: /space/cognito/5/users/raij/subjects_mri/ >> surfer: not in "scripts" dir ==> using cwd for session root >> surfer: session root data dir ($session) set to: >> surfer: /autofs/space/cuzco_002/users/raij/avml_fmri_mctogether >> surfer: Reading header info from >> /space/cognito/5/users/raij/subjects_mri//fsaverage/mri/T1.mgz >> reading group avg surface area 822 cm^2 from file >> surfer: vertices=163842, faces=327680 >> INFO: bvolumeRead: min = 0, max = 0 >> *** glibc detected *** corrupted double-linked list: 0x060b7db0 >> *** >> Abort >> >> Oddly enough, on machine ai, if I leave out the -timecourse part of the >> command line, the FreeSurfer window opens with the correct overlay and I >> can scroll through conditions and time points. Further, if I then >> manually >> load the timecourse from File/Load Time Course... menu, this works >> giving >> the time course display just as it should >> >> Even more oddly, on machine inv (which is spanking new and has lots of >> RAM >> etc) even the above basic command line with only loading the overlay >> gives >> the above glibc error. >> >> I have 8 subjects * 66 labels = timecourses of 528 labels to extract, >> which makes this clearly a script job - the only practical solution >> would >> be to find a way to make the command line work. >> >> Suggestions? For example, could it be that this has something to do with >> nvidia drivers? >> >> Thanks, >> >> Tommi >> >> --- >> Tommi Raij, M.D., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] selxavg-sess error
Hi Doug, selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -noomnibus exits with the error: ... Saving offset to group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat Slice 1, 77.2438 -- ??? Error using ==> minus Matrix dimensions must agree. Error in ==> fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]); >> ??? Undefined function or variable 'r'. >> quiting matlab -- ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): selxavg failed I suspect this may have to do that, for each of the seven subjects, there are three runs with an unequal number of TRs. Oddly enough, the same analysis worked in March 07. Is there a way to make this analysis work again? I am only interested in BOLD% signal change (FIR waveforms) so comparing runs with different numbers of TRs should be legal. What I would like to do is to calculate a single fixed effects group analysis where each of the three run types is output as its own category (the paradigm files are coded to allow that). Only runs that have the same number of TRs are collapsed across subjects. (Running three separate analyses, one for each run type, would not help, as we need the output to be in a single block with multiple categories, just as in our earlier analysis) Or maybe the error has to do with something else... my matlab setup.m should be fine to my knowledge. machine: cuzco nmr-dev-env (same error with the standard edition) cd /space/cuzco/14/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Thanks!!! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] selxavg-sess error
Improving... now selxavg-sess finishes without error, and even mkcontrast-sess and stxgrinder-sess seem to work (see below for command lines). The output seems to be in .nii format though, which is something of a problem for the rest of our custom analysis stream (our matlab routines can only read and write the previous .bhdr/.bfloat). However, as a more fundamental problem, now the analysis crashes at func2sph-sess (again, the same commands worked in April): mkcontrast-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -rmprestim -contrast A1-REST -a 1 -c 0 (etc. - more contrasts) stxgrinder-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -all -sf sessid7 -df sesspar ERROR: [cuzco:avml_fmri_mctogether] (nmr-dev-env) func2sph-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -trgsubject fsaverage -projfrac 0.3 -- func2sph-sess logfile is /autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/log/func2sph-sess.log -- - - Session: avml10_session_BRISI04 1/7 Mon Oct 8 02:00:29 EDT 2007 Mon Oct 8 02:00:29 EDT 2007 Filesystem 1K-blocks Used Available Use% Mounted on /local_mount/space/cuzco/14 100115936 63345920 36770016 64% /autofs/space/cuzco_014 Using Float2Int = round /autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04/bold mri_vol2surf --srcvol group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h --src_type bfloat --srcreg register.dat --trgsubject fsaverage --mapmethod nnfr --hemi lh --surf white --surfreg sphere.reg --out /autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04/bold/group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/sph/h-lh --out_type bfloat --float2int round --interp nearest --projfrac 0.3 can't find file group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h_000.hdr (last resort);bailing out on read srcvol = group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h srctype = bfloat srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.3 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 ERROR: could not read group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h as type 9 ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): vol2surf failed [cuzco:avml_fmri_mctogether] (nmr-dev-env) Thanks for your help in adavance, Doug! -Tommi > This should be fixed in both dev and stable on the next update > > [EMAIL PROTECTED] wrote: > >>Hi Doug, >> >>selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf >>sessid7 -df sesspar -noomnibus >> >>exits with the error: >> >>... >> Saving offset to >>group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat >>Slice 1, 77.2438 -- >>??? Error using ==> minus >>Matrix dimensions must agree. >> >>Error in ==> fast_selxavg at 439 >>extreg = extreg - repmat(mean(extreg), [ntrs 1]); >> >> >> >>>>??? Undefined function or variable 'r'. >>>> >>>> >> >> >> >>>>quiting matlab >>>> >>>> >>-- >>ERROR: fast_selxavg() failed\n >>ERROR >>(/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): >>selxavg failed >> >>I suspect this may have to do that, for each of the seven subjects, there >>are three runs with an unequal number of TRs. >> >>Oddly enough, the same analysis worked in March 07. Is there a way to >> make >>this analysis work again? I am only interested in BOLD% signal change >> (FIR >>waveforms) so comparing runs with different numbers of TRs should be >>legal. What I would like to do is to calculate a single fixed effects >>group analysis where each of the three run types is output as its own >>category (the paradigm files are coded to allow that). Only runs that >> have >>the same number of TRs are collapsed across subjects. >> >>(Running three separate analyses, one for each run type, would not help, >>as we need the output to be in a single block with multiple categories, >>just as in our earlier analysis) >> >>Or maybe the error has to do with something else... my matlab setup.m >>should be fine to my knowledge. >>
[Freesurfer] fMRI raw data time course
Hi Doug, I am troubleshooting an fMRI measurement and would need to see the raw data time course. I have previously used sliceview-sess for this purpose, but for some reason I can no longer make it work. Well, sliceview-sess itself opens fine if I define the analysis and contrast names, but pushing "r" has no effect (should evoke raw data display), and the command line raw data request gives a vague error. I already analysed the data in both bhdr and nii formats, without improvement (a time point exclusion file was used during analysis). -v1 or -v2 makes no difference. Any suggestions would be much appreciated! Bests, Tommi on machine cuzco nmr-std-env (same problem with nmr-dev-env) cd /space/cuzco/1/users/raij/avml_fmri_mctogether/avml14_session_BRISI12/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT avml14 [cuzco:avml14_session_BRISI12] (nmr-std-env) sliceview-sess -sf sessid -df sesspar -raw 011 -motioncor -- sliceview-sess logfile is /autofs/space/cuzco_001/users/raij/avml_fmri_mctogether/avml14_session_BRISI12/log/sliceview-sess.log -- INFO: no slice specified, assuming mosaic grep: /autofs/space/cuzco_001/users/raij/avml_fmri_mctogether/avml14_session_BRISI12/session.info: No such file or directory avml14_session_BRISI12 -- /autofs/space/cuzco_001/users/raij/avml_fmri_mctogether/avml14_session_BRISI12 yakview -i /autofs/space/cuzco_001/users/raij/avml_fmri_mctogether/avml14_session_BRISI12/bold/011/fmc -r /autofs/space/cuzco_001/users/raij/avml_fmri_mctogether/avml14_session_BRISI12/bold/011/fmc -sn mos -thmin 2 -thmax 7 -title avml14_session_BRISI12 -v1 -mgh -- yakview: \$Id: yakview,v 1.11.2.1 2007/10/05 20:42:55 greve Exp $ ERROR: cannot find [cuzco:avml14_session_BRISI12] (nmr-std-env) --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] EEG source localization?
Hi Andrea, There is a FreeSurfer compatible MEG/EEG analysis package that can constrain the source space to the cortical mantle. Please see http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php Bests, Tommi > I have used freesurfer in the past for functional imaging data. Can > source > localization also be completed for EEG data utilizing the available > anatomic > MR images? > > Thanks, > > Andrea > > -- > Andrea R. Seisler > Laboratory Manager > Human Electrophysiology Facility > Social, Life, & Engineering Sciences Imaging Center > 120 Chandlee Laboratory > The Pennsylvania State University > University Park, PA USA 16802 > Phone: 814-865-6774 > Email: ar...@psu.edu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Tommi Raij, M.D., Ph.D. TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] Version conflict in FS-FAST or unpacksdcmdir?
Dear Free Surfers, I wonder if something went wrong with transitioning FS-FAST and/or unpacksdcmdir from 4.5 to 5.0. Our functional analysis stream is set to work in 4.5 and it was working fine. However, since the default version was changed to 5.0, our analyses have stopped working despite that we source /space/freesurfer/nmr-stable4-env We receive multiple errors (see ERROR 1 and ERROR 2 below) that start already at preprocessing (ERROR 1 below). For example, functional data from Bay 4 that was unpacked with unpacksdcmdir before the version shift goes through preprocessing just fine (even today), whereas if I re-unpack the exact same raw data the preprocessing fails. Details: cd /space/avml/3/users/bletham/ADA_fMRI/AD003/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ setenv SUBJECT AD003_FSvs4.5 nmr-std-env # this takes us to version 5.0 of course so we also give source /space/freesurfer/nmr-stable4-env ** ERROR 1: ** preproc-sess -sf subjectname -df sessdir -fwhm 6 -sliceorder siemens -inorm -force ... some messages ... >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Error using ==> fmri_svbfile Too many output arguments. Error in ==> fast_svbslice at 71 err = fmri_svbfile(yslice,fname); Error in ==> MRIwrite at 83 err = fast_svbslice(mri.vol,fstem,[],outbext,bmri); >> >> -- ERROR: output not created ERROR: mc-sess failed ** ERROR 2: ** For data that was unpacked before the version change, now when we try to run analyses under vs 4.5 we also receive another type of error at selxavg3-sess that seems to be related to version numbers: ... Computing CES Magnitude AV8VT-REST J=13 - Computing CES Magnitude Saving h.dat to /autofs/space/avml_003/users/bletham/ADA_fMRI/AD003/bold/FIRsm6pf2_taumax20/h.dat ??? Reference to non-existent field 'Version'. Error in ==> fmri_svdat3 at 35 if(hd.Version == 2) Error in ==> fast_selxavg3 at 1039 fmri_svdat3(fname,hd); >> -- ERROR: fast_selxavg3() failed\n Any suggestions? Anything and everything of course most welcome! Best regards, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] changing f.nii nframes
Dear Free Surfers, I am analyzing fMRI time series that were reconstructed offline (GRAPPA data that needed some artifact corrections, long story). Unfortunately, the offline reconstructed f.nii do not include proper header info. I think I was able to set the orientations correctly using mri_convert, but now FSFAST preprocessing (specifically, mc-sess) fails because the headers say that the number of TRs (number of full volume acquisitions) in the measurement is 1, whereas in fact the correct value is 316. I could not find a tool that could change the "nframes" value (mri_convert can adjust many other things but not this one it seems). Any suggestions? Bests, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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] CSF masks
Hi, We are trying to create a CSF volume mask from structural MEMPRAGE T1 data (we also have ME FLASH 5/30 ->PD if needed). We are interested in two CSF compartments: - "superficial" CSF outside grey matter and inside inner skull - "deep" CSF inside ventricles Is there a way to simply extract these from aseg.mgz or how should we go about this? Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] CSF masks
Thanks Bruce! However, as you suspected this does not seem to work: mri_extract_label mri/aseg.mgz 24 mri/mask_code24.mgz gives a tiny volume of a couple of hundred voxels in the middle of the brain (part of 3rd ventricle). I assume here that code 24 is the correct code for all CSF in aseg.mgz. I guess an alternative would be to take the volume of inner skull minus the volume of everything including and below pial surface. How would one go about doing that? Or would you suggest other ways? Bests, Tommi > Hi Tommi > > you can use mri_extract_label to pull out the labels you want, but the > sulcal CSF labels may not be great since the manual labeling that is the > basis of the aseg was done on only T1 images. > > cheers > Bruce > > On Wed, 8 Dec 2010 > r...@nmr.mgh.harvard.edu wrote: > >> >> Hi, >> >> We are trying to create a CSF volume mask from structural MEMPRAGE T1 >> data >> (we also have ME FLASH 5/30 ->PD if needed). We are interested in two >> CSF >> compartments: >> >> - "superficial" CSF outside grey matter and inside inner skull >> - "deep" CSF inside ventricles >> >> Is there a way to simply extract these from aseg.mgz or how should we go >> about this? >> >> Thanks! >> >> -Tommi >> >> --- >> Tommi Raij, M.D., Ph.D. >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> Bldg 149, 13th St >> Charlestown, MA 02129 >> U.S.A. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ Freesurfer mailing list Freesurfer@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] Question: FS-FAST mc-sess -perrun
Hi Doug, The issue is motion correction in FS-FAST. The environment is nmr-dev-env. mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)". 1. Does "targ=mid" implicate that the target, within each run, is the image half way through the run? 2. Does this equal to using the mc-sess -rlf runlistfile flag, and changing the contents of the runlistfile to match each of the run numbers, one at a time? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question: FS-FAST mc-sess -perrun
mc-sess with -perrun failed with the output: targstem: Undefined variable. *** Bug report: *** on machine ai source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri cd /space/cognito/5/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT which mc-sess /usr/local/freesurfer/dev/fsfast/bin/mc-sess mc-sess -sf sessid -df sesspar -perrun Logfile is /autofs/space/cognito_005/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT/log/mc-avml19_session_BRISI13_ISI1TR_BERT-bold.log --- /autofs/space/cognito_005/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT RunList: 004 005 006 targstem: Undefined variable. Notice that I am using the building 120 "cognito" installation where: /usr/local/feeesurfer = /space/cognito/24/opt/freesurfer/centos4.0 Bests, Tommi > > [EMAIL PROTECTED] wrote: > >>Hi Doug, >> >>The issue is motion correction in FS-FAST. The environment is >> nmr-dev-env. >> >>mc-sess flag -perrun is documented like this: >>"MC each run separately (targ=mid)". >> >>1. Does "targ=mid" implicate that the target, within each run, is the >>image half way through the run? >> >> > Yes > >>2. Does this equal to using the mc-sess -rlf runlistfile flag, and >>changing the contents of the runlistfile to match each of the run >> numbers, >>one at a time? >> >> > Almost. Method #2 will use the first image instead of the middle image. > > doug > >>Thanks, >> >>Tommi >> >>--- >>Tommi Raij, M.D., Ph.D. >>MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >>Bldg 149, 13th St >>Charlestown, MA 02129 >>U.S.A. >> >>[EMAIL PROTECTED] >>___ >>Freesurfer mailing list >>Freesurfer@nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST spatialsmooth-sess error
Hi Doug, spatialsmooth-sess failed on the second run (out of 6 runs) with the output: ... ERROR: failure writing /tmp/ipfsl_19705/fmc.img as volume type 16 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold mri_convert 005/fmc.bhdr /tmp/ipfsl_19705/fmc.img --out_type analyze4d ERROR: mri_convert failed ERROR: ipfsl failed Two explanations come to mind: A. Each number has a different number of TRs. Does the ntrs value in the seq.info (inside bold dir) have to match the actual number of TRs in each run? I here tried to smooth all runs in one step... obviously this is not going to work if the ntrs value has to be correct. Should I process the runs one at a time with -fsd NNN and adjust the seq.info ntrs value between? B. The number of images was big = 666 / 1095 / 1741 per run (2 runs each size). Did the scratch disk or mri_convert run out of memory? *** Detailed problem report: *** on machine ai source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri cd /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT which mc-sess /usr/local/freesurfer/dev/fsfast/bin/spatialsmooth-sess spatialsmooth-sess -sf sessid -df sesspar -fwhm 6 -i fmc -o ifmcsm6 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT Tue Feb 28 18:50:28 EST 2006 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT RunList 004 005 006 009 010 011 -- /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold ... Notice that I am using the building 120 "cognito" installation where: /usr/local/feeesurfer = /space/cognito/24/opt/freesurfer/centos4.0 Thanks, Tommi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS-FAST registration across sessions
Hi Doug, I tried the technique you suggested for re-sampling functional volumes from different sessions but from the same subject (and scanner) into the same space, using mc-sess. To clarify, here we have a situation where the same brain is scanned in the same scanner on more than one occasion (in this particular example, the subjects were taken out of the scanner half way through the lengthy functional recordings for 20 minutes to rest). Obviously the head position and rotation are almost always quite different in session 1 than session 2. It would make building contrasts and combining results across sessions (but within subjects) much more straigthforward if the functional volumes from the two "sessions" could be re-sampled into the same space. I put all my runs (2 sessions, 3 runs each = total of 6 runs) from the same subject and scanner in one bold directory, ran mc-sess, and got confusing results. When I check the alignment with tkregister2, the result looks very bad - the volumes from different sessions are clearly not in the same space (1-3 cm difference). However if I ignore the fact that the runs do not appear to be aligned, and run spmregister-sess just once for all runs (hence there is only one register.dat file) and then check the registration with tkregister-sess, runs from both sessions seem to be similarly and well aligned with the hires anatomicals. Obviously the mis-alignment from mc-sess should be inherited to all following steps, so I must be doing something wrong. I wonder where the mistake is? Am I misusing the tkregister 2 command (see below)? Or is this a bug? *** Here are the specifics: *** Session 1 = runs 004, 005, 006 Session 2 = runs 009, 010, 011 on machine ai source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT avml19 cd /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT # MOTION CORRECT mc-sess -sf sessid -df sesspar # SPATIAL SMOOTHING AND INORM, OUTSTEM = ifmcsm6 spatialsmooth-sess -sf sessid -df sesspar -fwhm 6 -i fmc -o ifmcsm6 # CHECK ALIGNMENT OF RUN 004 VS. 009 WITH TKREGISTER2 - LOOKS BAD tkregister2 --targ bold/004/fmc.bhdr --mov bold/009/fmc.bhdr --regheader --reg /tmp/junk.reg # RUN SPMREGISTER ONCE FOR ALL RUNS TOGETHER DESPITE THAT ALIGMENT APPEARS BAD spmregister-sess -sf sessid -df sesspar -funcstem fmc # CHECK REGISTRATIONS (ONLY ONE bold/register.dat FILE) - LOOKS OK FOR BOTH, AND VERY SIMILAR FOR RUNS 004 AND 009??? tkregister-sess -sf sessid -df sesspar -funcstem fmc -run 004 & tkregister-sess -sf sessid -df sesspar -funcstem fmc -run 009 & --- Also, the defaults for spmregister-sess and tkregister-sess funcstems are "f". I hope, because my setup does not overwrite the mc-sess output with the output of spatialsmooth-sess, that I am correct in using the "fmc" stem instead of "f"? If I have understood corectly, this has the advantage that I can register motion corrected but not spatially smoothed functional data, which might(?) at least theoretically give better results than registering functionals without motion correction... though the advantage might be too small to be relevant compared to less than perfect registration accuracy. Any thoughts regarding this? I tried the registration with the stem "f" as well, and the problems remained the same, so at least this does not seem to be the cause. Thanks, Tommi > hi doug > > i think i have actually already done what you suggest as my bold directory > consists of all the retinotopy runs (in subdirs 001-010). this is the 'ls' > of > the bold directory: > > 001/ 003/ 005/ 007/ 009/ register.dat same-sess-reg.dat seq.info > 002/ 004/ 006/ 008/ 010/ rtopy/scripts/ > > i ran the motion correction from the study directory as: >>mc-sess -sf sessid -df sesspar > and it completed successfully. > > -so will that have aligned all the runs together? if so, what can explain > the > fact that the field sign map is not continuous when overlaid on the cortex > and > shows gaps in the blue/yellow colouring? > > thanks! > > jane > > > In message <[EMAIL PROTECTED]> Doug Greve > <[EMAIL PROTECTED]> writes: >> >> You can try putting all the runs into a single bold directory. The >> motion correction will (do it's best to) align them. >> >> doug >> >> >> >> >> >> >> Jane Aspell wrote: >> >> >Hi >> > >> >My question was asked last year by Tommi Raij (see email pasted below) >> but I >> >couldn't find a reply to it in the archives. I am analysing retinotopy >> data >> >that was collected over several sessions but I cannot see how to >> register >> >scans from multiple session
[Freesurfer] Q: tkregister2 coronal/sagittal/horizontal discrepancy
Dear Fellow Surfers, After doing a reconstruction with the 3.0 Freesurfer stable version, I checked the Talairach auto-registration with tkregister2. The registration seemed fair enough. However I noticed a strange thing that has not caught my attention before - maybe this a property of the program and/or was there already earlier, maybe it is new, maybe it is a bug, or perhaps my volume is corrupt. The problem/property is observed within the original (target) volume. After launching tkregister2, if I click inside the target volume, the red cursor moves to that location and other orientations (coronal/sagittal/horizontal) slices also change accordingly (the sliders move). If I have understood correctly, the idea would be that the cursor shows the crossing in all 3 orientations. However if I look at the brain structure in the three different orientations where my cursor is, it is clearly different in all three images. For example, if I pick a mid-sagittal view and place the red cursor in the thalamus between AC and PC, and then click the "sagittal" button, the cursor is clearly higher (towards top of the head) in the interhemispheric fissure. If I click the "coronal" button, the cursor is in the frontal lobe between the hemispheres (ie much more anterior than the other views). Is this the way the program is supposed to work, or is this a bug, or is my volume plain corrupted? *** Here are the specifics: *** on machine ai source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT avml07 cd /space/cognito/5/users/raij/subjects_mri tkregister2 --mgz --s avml07 --fstal ... and there you go, click away... Thanks for your advice in advance, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mean & SD over ROI in a FIR analysis (several timepoints)
We are trying to calculate mean and SD over all the spatial (vertex) points included in a single functionally defined ROI/label. Bottom line, the biggest problem is that we do not know which tool to use to read all timepoints/frames of the hemodynamic waveforms (of all the vertex points included in the label, one at a time) into matlab. For details, please see below. Problem 1: We tried to use mri_label_vals but this gives only one value per vertex point. However this is a FS-FAST FIR analysis with a time window of 16 frames/TRs (of which two are prestimulus) so we should get 16 values for each vertex point in order to draw a BOLD time course. So we need a reader that will produce the functional stat values for all the time points, separately for all vertices included in the ROI. Problem 2: We would need to subtract the mean prestimulus baseline values from all 16 time points in order to set a (mean) zero baseline. This is necessary to decrease the voxel-to-next-voxel variability that is large in fMRI data. This of course has to be done before calculating the mean and SD values over the ROI. We did use mkcontrast-sess -rmprestim - does this result in that the baseline is already subtracted in the values (for each vertex point separately)? There are typically about 600 single vertex points in a label so saving them manually one by one as ASCII and then combining them is not feasible. As a separate but complicating issue, we have 6 simple contrasts (condition N minus REST, with names such as A-REST, V-REST, etc) and 2 slightly more complicated contrasts (condition 1 plus condition 2 minus condition 3). Loading and overlaying the ROI mean +- SD curves for each contrast separately increases the work load 6-fold. We have multiple subjects in six different conditions, each with multiple ROIs, and 6 simple contrasts, leading to thousands of BOLD waveforms - any practical application should automatically load all 6 contrast HDR waveforms and overlay them in a single window (exactly as sliceview-sess, tkmedit, and tksurfer do when you load time course - except that in these programs the time courses are displayed for only a single voxel at a time). Any suggestions how this could be achieved? Example data/analysis can be found in /space/cognito/5/users/raij/avml_fmri/avml12_session_BRISI07_ISI1TR_BERT There are two analyses here - here we are interested in the FIR analysis: ISI1TR_BERT_ERFIRsm6pf5tpefsub ... and the variables are setenv SUBJECT avml12 setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ Any advice would be greatly appreciated! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with tkmedit Tools/fMRI/Select Contiguous Voxels by Threshold
Hi guys, I use tkmedit (current MGH beta release) to manually select my ROIs. I overlay the functional contrast, move the cursor inside the cluster of interest, and then go Tools/fMRI/Select contiguous voxels by threshold (after setting the threshold for a proper value of course). Works great, the volume turns green, and can be saved as a label. But only for positive contrast values. When I point the cursor inside a negative cluster and Select Contiguous Voxels by Threshold, nothing will turn green. Saving the label will result in a file with contents zero. Reversing values in "Configure functional overlay" does not help. Same problem with the alpha release. However, selecting with "Select contiguous voxels by Func Value" can pick also negative clusters. But then it is more difficult to control the threshold of course - I would prefer to use the Threshold. Any suggested ways around this? Or am I just doing something plain wrong? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FS-FAST Registration Question: registration across sessions within subjects
Hi Doug/All, This is a question about registering several functional scans from the same subject in the same space. The functional scans are from different sessions, so even if the slice recording parameters are identical, the head will inavoidably be in different locations and with different rotation. The data have already been collected, so we cannot use any on-line corrections. Four different techniques come to mind that could be used to achieve this, but I would expect that the accuracy of the methods varies a lot. Optimally IMHO one should register the different functional runs with respect to each other directly, simply because the EPI images are very similar with respect to each other (or at least their T1 contrast is). The high-resolution structural image is very different compared to the EPI images so functional-to-structural registration is expected to be much more inaccurate. Here are the four different techniques (please tell me if you can think of more): 1. One possibility would be to use mc-sess for all runs from the same subject (place all the runs from the different sessions in a single "bold" directory and just run mc-sess). Possible problem: If I have understood correctly, mc-sess only corrects for motion within slices. Therefore the different head rotations would make this technique very inaccurate. Or does there exist an updated version of mc-sess that could handle even large displacements and rotations? 2. A second possibility would be to use one of the automatic functional-to-structural registration programs and register each functional run to the same hires structural image. However, based on the discussion above, there are expected to be inaccuracies in the functional-to- structural registration that could be large enough to make comparisons across the functional sessions meaningless (i.e., the differences would mainly be driven by inaccuracies in the registration). 3. A third possibility would be to use the same technique as for registration across subjects, i.e., resampling the different runs from the same subject into a spherical space calculated from this specific subject. Again this is just as variety of registration from functional to structural, and would be expected to provide suboptimal results. 4. A fourth possibility would be to find a method for registering all the functional images in a single space with respect to each other, e.g. by picking one of the functional sessions as the target space and resampling all other functional sessions from this subject into this space (without using the hires structurals at all). I guess this would be kind of motion correction but capable of handling rotations. If such a tool exists, it might be more accurate than any of the methods above, simply because the functional images are more similar compared to each other than compared to the subject's hires structural image. Any ideas/suggestions which method would give the most accurate result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_pmake version issue
Dear FreeSurfers, I am trying to update an mris_pmake command line that works with the pub v5.3.0 version with a new command line that works with pub v6.0.0 version. The purpose is to compute the distance between two vertex points on the pial surface using the cvs_avg35_inMNI152 brain. We are using CentOS (6.6 on the workstation running FS v5.3.0 and 7.4 on the workstation running FS v6.6.0) outside Martinos Center. nmr-std-env setenv SUBJECTS_DIR /usr/pubsw/packages/freesurfer/subjects setenv SUBJECT cvs_avg35_inMNI152 Old command line (gives a reasonable result on v5.3.0): mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --surface0 pial --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:121981,endVertex:132633 Start->End vertices [ 121981->132633 ] Total path cost [ 29.668283 ] If I try to run this on v6.0.0, I receive the error: mris_pmake: unrecognized option '--surface0' I first tried removing --surface0 option, but then the error becomes mris_pmake: unrecognized option '--curv0' I then tried removing the --curv0 and eventually --curv 1 options as well, but these gave more similar errors (unrecognized option) or core dumped. Looking at older posts on the FreeSurfer list, I tried removing all three --surface0 --curv0 --curv 1 options, but this gives a clearly incorrect result where the startVertex and endVertex values are apparently not read from the command line: Start->End vertices [ 0->0 ] Total path cost [ 0.00 ] I tried renaming --surface0 to --surface and --curv0 to --curv, as it seems that some of the options have been renamed, and to some degree this worked as there were no more 'unrecognized option' errors. However, the result is still Start->End vertices [ 0->0 ] Total path cost [ 0.00 ] Any suggestions would be greatly appreciated. Btw the command line documentation (mris_pmake --help) does not seem to be quite match the version distributed with FS v6.0.0, at least when it comes to the option names for surface and curve, and if there are separate definitions for 0 and 1. Thank you! Best regards, Tommi Raij ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Older tksurfer and tkmedit (FS version 5.0.0) fail to launch: glut issue?
Dear Surfers, I am trying to launch tksurfer/tkmedit in the stable 5_0_0 environment in the Martinos network, but this fails with glut segmentation errors. FS version 6 tksurfer works on the same machine and data, but I need to create some figures that match version 5. We already tried with a different user and a few years older linux box, same issues. Any suggestions would be greatly appreciated! For example, is there a variable that we could set to point to an older OpenGL version? (My LD_LIBRARY_PATH has not been set, and my PATH does not include anything pointing to /usr/lib or /usr/lib64) Details: on machine rukki (locally at terminal): setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env cd $MY_SUBJECTS_DIR Checking version: freesurfer ... You are running this version of FreeSurfer: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 echo $FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 cp -r $FREESURFER_HOME/subjects/fsaverage $MY_SUBJECTS_DIR/. chmod -R 777 fsaverage [rukki:sphsm10-ffx] (nmr-stable5.0-env) tksurfer fsaverage lh inflated subject is fsaverage hemiis lh surface is inflated surfer: current subjects dir: <$MY_SUBJECTS_DIR> surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: <$MY_SUBJECTS_DIR> Reading image info <$MY_SUBJECTS_DIR>/fsaverage) Reading <$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz surfer: Reading header info from /<$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz [rukki:sphsm10-ffx] (nmr-stable5.0-env) ... after which there is no screen output. The file xdebug_tksurfer was generated: [rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tksurfer Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut [rukki:sphsm10-ffx] (nmr-stable5.0-env) [rukki:sphsm10-ffx] (nmr-stable5.0-env) echo $DISPLAY :3 setenv DISPLAY :0 does not fix the issue (results in GLUT: Fatal Error in tksurfer.bin: could not open display: 0) I also tried fsaverage4, fsaverage5, fsaverage6, and bert, copied from the same folder into my $SUBJECTS_DIR, same result. The issue is not specific to tksurfer: tkmedit -f fsaverage/mri/T1.mgz === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : [rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tkmedit tkmedit started: Wed Aug 7 16:54:21 2024 tkmedit.bin -f fsaverage/mri/T1.mgz $Id: tkmedit.c,v 1.341.2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5_0_0 $ Set user home dir to ($MY_SUBJECTS_DIR) Set subject home dir to fsaverage/mri/T1.mgz Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x3447db0, isSource=./fsaverage/mri/T1.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=fsaverage/mri/T1.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=tkmedit.bin ) 02: Loading volume fsaverage/mri/T1.mgz 01: main() 01: Parsing command line arguments 00: 00: [rukki:sphsm10-ffx] (nmr-stable5.0-env) My OpenGL version: [rukki:sphsm10-ffx] (nmr-stable5.0-env) glxinfo | grep "OpenGL version" OpenGL version string: 4.6.0 NVIDIA 550.54.14 The other machine we tried had OpenGL version 4.6.0 NVIDIA 535.54.03 Thank you! Best regards, Tommi --- Tommi Raij, MD, PhD Director, TMS Clinical Research MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th st Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] Pial surfaces include cerebellum - unable to fix with manual edits
Dear Surfers, I have a case where recon-all labels cerebellum as cerebral white matter (aparc+aseg.mgz) and the pial surfaces therefore include the cerebellum. The error has been resistant to attempts to fix the situation with manual edits to $SUBJECT/mri/brain.finalsurfs.mgz and re-running autorecon3 (with or without autorecon2). Specifically: Without manual edits, recon-all hangs at the stage: ... CORRECTING DEFECT 0 (vertices=34440, convex hull=821, v0=4192) XL defect detected... ... After exiting with Ctrl-C, brain.finalsurfs.mgz include cerebellum, and the pial surfaces include cerebellum. I guess the "defect" FS is trying to correct is the cerebellum that was mislabeled. My manual edits to brain.finalsurfs.mgz consisted of removing cerebellum by painting with brush value = 1 (freeview voxel edit tool). Thereafter, I recomputed autorecon 3: recon-all -autorecon3 -s $SUBJECT -no-isrunning With this, recon-all finishes "without error" but the recomputed aparc+aseg.mgz still thinks cerebellum is cerebral white matter and the pial surfaces again include cerebellum. This is with Martinos Center stable version 6. Any suggestions would be greatly appreciated! Also happy to send a link to the original T1 and recon-all results if you would like. Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th st Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
