[Freesurfer] ERROR: QdecGlmDesign::Create: zero factors!
Dear freesurfer user, I'm new in this freesurfer and i want to analysis of the thickness of two groups, dementia and normal. I was trying to use qdec but when i pressed analyze button, there was some message at the bottom, which is Error during design creation. At the same time, on the terminal, the following message came up. ERROR: QdecGlmDesign::Create: zero factors! For details, See below. Please let me know what the problem is. Thanks. *M.J. * Reading /Applications/freesurfer/tktools/tkUtils.tcl Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /Applications/freesurfer/subjects/qdec.table.dat... Number of columns: 3 fsid column:1 Number of factors: 2 Number of subjects: 10 Reading discrete factor levels from config file /Applications/freesurfer/subjects/diagnosis.levels AD Normal done. Data table /Applications/freesurfer/subjects/qdec.table.dat loaded. Verifying subject data..Subject verification complete. Input table: /Applications/freesurfer/subjects/qdec.table.dat Subj#, SubjID, Data... 1 a1002 AD 75.00 2 a1003 AD 63.00 3 a1009 AD 71.00 4 a1015 AD 80.00 5 a1019 AD 75.00 6 n1004 Normal 72.00 7 n1005 Normal 71.00 8 n1006 Normal 57.00 9 n1007 Normal 62.00 10 n1008 Normal 62.00 1 diagnosis discrete 2 1 AD 2 Normal 2 age continuous 0 Continuous Factors: Mean: StdDev: --- - --- age68.800 7.361 Number of subjects: 10 Number of factors:2 (1 discrete, 1 continuous) Number of classes:2 Number of regressors: 4 Data table loading completed successfully. SUBJECTS_DIR is '/Applications/freesurfer/subjects' ERROR: QdecGlmDesign::Create: zero factors! ___ 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] Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file
Hi Yoon, when you run the script kvlQuantifyHippocampalSubfieldSegmentations.sh, it goes along the volumeStats_left.txt and volumeStats_right.txt to build a large table with all the volumes. The output files (nonPartialVolumeStatsLeft.txt/nonPartialVolumeStatsRight.txt) should be in your subjects directory $subject. Regarding the partial volume segmentation, it's not fully implemented / tested yet. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Yoonho Chung yoonho.ch...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 15, 2014 10:33:19 PM Subject: [Freesurfer] Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file Hi, I am running Hippocampal subfield processing stream and I think I got all the appropriate posterior_*.mgz files I need to get the stats, but I am not seeing nonPartialVolumeStatsRight.txt anywhere as described in the wiki under $subjectsdir. What I am seeing is volumeStats_left.txt and volumeStats_right.txt files under the $subject/mri directory and one of the text files look like this. volumeInVoxels: Left-Hippocampus: 2616.97 left_presubiculum: 4050 left_CA1: 2880.55 left_CA2_3: 8120.59 left_fimbria: 212.439 left_subiculum: 5985.02 left_CA4_DG: 4459.07 left_hippocampal_fissure: 358.59 - If I look at the end of the hippo-subfields.log file, it is saying it is skipping the partial volume segmentation (see below). --- ... Debug: Off Observers: none Matrix: -0.5 0 0 0 0 0.5 0 -0.5 0 Offset: [41.7047, -40.8148, -4.10007] Center: [0, 0, 0] Translation: [41.7047, -40.8148, -4.10007] Inverse: -2 0 0 0 0 -2 0 2 0 Singular: 0 spacing: [0.5, 0.5, 0.5] origin: [41.7047, -40.8148, -4.10007] direction: -1 0 0 0 0 1 0 -1 0 done! Skipping the partial volume segmentation part --- Can please someone tell me what I am missing? Also, what do I need to do to extract the values to a spreadsheet? Should I use asegstats2table? under '-help' it doesn't say which options it should be used to get the subfields. Thank you so much for the help in advance. Cheers, Yoon ___ 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] load_nifti.m - empty header
Dear Freesurfers, I am struggling with a very basic step at the very beginning of my processing pipeline. This is what I've done: registered BOLD to anatomical data using bbregister, results checked with tkregister2 - all seems fine. Then I want to project BOLD data to the surfaces using mri_vol2surf - no error so far. BUT when trying to load the mri_vol2surf output into matlab (load_nifti.m) I get this error: *??? Attempted to access hdr.dim(2); index out of bounds because numel(hdr.dim)=0.* *Error in == load_nifti_hdr at 121* *if(hdr.dim(2) 0)* *Error in == load_nifti at 80* *hdr = load_nifti_hdr(niftifile);* It seems that the hdr struct is completely empty. Thanks in advance for any kind of help, have a nice week, Nadine ___ 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] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoon - The update is here: http://freesurfer.net/fswiki/Tracula#Updates There will also be a new freesurfer release in the next couple of months, but I don't anticipate making more changes to longitudinal tracula before that, so this should be the same as in the future 5.4 version. a.y On Wed, 23 Jul 2014, Yoonho Chung wrote: Thank you for your input. Before we go ahead and reprocess our recon and DTI data with FS v 5.3 we were wondering if you plan an update on the TRACULA DTI longitudinal stream anytime soon. I think I saw somewhere in the email chain that this is likely to happen soon with additional features and bug fixes. If so, I think it would be worth the wait. Thank you! Yoon On May 22, 2014, at 5:37 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Chung wrote: Thanks for the quick response! If I already have all the T1 data processed using recon-all with FS v5.2, do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - without having to do the recon-all again for the T1 data? It is because I am also experiencing DTI longitudinal error due to the OS issue (according to other threads). And if possible, I would like to avoid having to redo all the recons if we have to switch it to v5.3. Thanks again! Yoon 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
Re: [Freesurfer] Tracula : Path not entirely in the white matter
Hi Emily - Yes, this is fine. I just meant that it shouldn't look like a single line. a.y On Thu, 24 Jul 2014, ebell...@uwm.edu wrote: Hi Anastasia, Just to be clear, is this what you mean by a more diffuse volumetric distribution. Here is a snapshot of the right inferior longitudinal fasiculous. I am just getting a better sense of what to look for in terms of bad vs. good tracts. Emily - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 16, 2014 4:54:29 PM Subject: Re: [Freesurfer] Tracula : Path not entirely in the white matter Hi Emily - This is not necessarily a problem. To make sure, you can check the output path.pd.nii.gz file from that specific tract. If it got stuck somewhere (e.g., because the brain mask is missing a bit of brain that this tract should go through) then the path.pd.nii.gz will look like a single curve rather than a more diffuse volumetric distribution. Hope this helps, a.y On Wed, 16 Jul 2014, ebell...@uwm.edu wrote: Hello, I was looking at a trac-all log file to get my bearings on what is being done and making sure things were done successfully, I did not get any errors for this subject but when I was looking at the right uncinate fasciculus: It would say Path from initial control points not entirely in the white matter and then it attempted to perturb control points. I noticed that for this tract, it did not say that it did not say sucess after how ever many control points. It just said that it reverted back to the initial control points. Do I then need to be concerned about the validity of this particular tract for this subject? Thanks, Emily ___ 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
Re: [Freesurfer] dmri_trk2trk issue
Hi Tommi - The input reference volume (--inref) should be in the same
space as the input .trk file, i.e., your individual's diffusion space. It
seems that you're using the individual's T1 space instead?
a.y
On Fri, 25 Jul 2014, r...@nmr.mgh.harvard.edu wrote:
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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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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Re: [Freesurfer] Diffusion analysis qs
Hi Rotem - It's hard to tell without zooming into some key areas, like corpus callosum and cingulum for example. The colors look ok (red and green, respectively) but it's hard to see how the lines look. a.y On Mon, 28 Jul 2014, Rotem Saar wrote: Dear Anastasia, I followed your suggestion: I calculated the FA maps in freesurfer using the script below (see last message): I did it with both the rotated and the not rotated gradient table. The FA maps were identical as u said. BUT ! - when I used the rotated gradient table in FSL and tried to create the FA MD maps (as in the first step of tracula), I got the attached results: http://tinypic.com/r/skzwqa/8 Does this map seems ok to u ? I think that something is wrong but can't specify what. I will appreciate your help here again:) Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: Dear Anastasia Michael, Thank u for your answers (I attached my last email and your answers at the end of this email. I still want to specify my question. If I only want to extract FA values using the following script (see script below), and I know that an angle was applied during the dMRI scans, should I use the rotated gradient matrix ? When I first analyzed 20 subjects with the gradient matrix that is published for a T3 Philips magnet (I also read the gradients from the dicom header - they were the same) I got reasonable results - but now I don't know what to think of them... source ~/Desktop/fs_script dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec To check results, run: tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii freeview -v/usr/local/freesurfer/subjects/Anatomy0207/mri/brain.mgz/usr/local/freesurfer/subje cts/Anatomy0207/DTI/fa.nii:reg=register.dat:colo rmap=heat:heatscale=.2,.2,1 tkmedit Anatomy0207?orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ ??? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc.mgz \ ??? --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ ??? --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ ??? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ ??? --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ ??? --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ ???/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:color map =lut mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz freeview -v/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz/usr/local/freesurfer/s ubjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap =lut mri_segstats --seg /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked It'd be nice if things were that simple, but! Although the pre-processing is done with FSL tools, tractography is done with locally written code. Some gradient sets may appear to work with FSL, but they won't work for us. For example, some dicom converters may perform a L-R flip as preparation for feeding the gradient vectors into FSL. We need the
Re: [Freesurfer] trac-all -prep problem
Hi Shantanu - It's stuck trying to initialize one of the tracts. You can check which tract it is, and then check the data to see if there's something wrong that would affect that particular tract (for example, if part of the brain that this tract goes through is cut off in the mask). a.y On Fri, 1 Aug 2014, Shantanu Ghosh wrote: Hi Freesurfer experts, I ran the command trac-all -prep -c dmrirc.txt on a bunch of subjects and all of them finished in ~90 minutes except one. This subject keeps on going into a seemingly endless loop. It has been running for almost 12 hours now. A section of the console output is reproduced below. What is the issue here, and how can this be solved? I am using the dev version on a Linux box. Thanks in advance for all help. Shantanu -- SAMPLE CONSOLE OUTPUT -- INFO: Distances between consecutive points in test subject's space are 11 11 10 10 10 WARN: Could not find satisfactory control point fit - try 1831 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 91 voxels Selecting 6 points on center streamline INFO: Minimum allowable distance between dominant points is 9 INFO: Minimum allowable curvature at a dominant point is 0.0283381 INFO: Points where local peeks in curvature occur are 106 105 67 (curv = 0.0284049) 112 108 77 (curv = 0.0450985) 115 108 98 (curv = 0.0526145) 113 104 116 (curv = 0.0460477) 107 103 128 (curv = 0.0759711) INFO: Intermediate dominant points are 103 98 50 112 108 77 114 108 89 115 108 98 107 103 128 105 106 145 INFO: Final dominant points are 103 98 50 112 108 77 114 108 89 115 108 98 107 103 128 105 106 145 WARN: Defaulting to equidistant dominant points WARN: Defaulting to equidistant control points INFO: Selected control points are 103 98 50 108 106 69 114 108 89 114 105 108 108 103 126 105 106 145 INFO: Distances between consecutive points are 21 21 19 19 19 INFO: Selected control points in test subject's space are 80 62 23 81 66 31 84 68 40 84 66 48 82 64 56 81 65 64 INFO: Distances between consecutive points in test subject's space are 9 10 8 8 8 WARN: Could not find satisfactory control point fit - try 1832 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels ___ 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] Tracula Missing Statistics
Hi Emily - The weighted average is the most reliable in practice, and it is also the proper statistical definition of mean (expected) value. It weighs the value of FA etc at each voxel with the probability of the tract going through that voxel. The cases that are missing stats may need to be rerun. I'm guessing that those will look like single curves if you view the path.pd.nii.gz volume. You can rerun them by using set reinit = 1 in the config file, and also specifying in the config file to run only the specific tract and specific subject. You'd have to rerun the -prior and -path steps only. a.y On Sun, 3 Aug 2014, Emily Louise Belleau wrote: Hello Tracula Experts, I noticed that for a few of my subjects, I am missing all Center statistics for FA, MD etc. for certain tracts like the left uncinate fasciculus for example. I am assuming this means that an optimal pathway was unable to be found? I do have the average and weighted statistics for these subjects. Should I consider excluding these subjects or should I try analyzing them again with different parameters? Additionally, I noticed that for a couple of my subjects, the Length Center (length of the highest probability pathway) is unusually short compared to the rest of the subjects? Is this a problem and do I consider excluding or tweaking the parameters for these subjects? Also, do individuals usually report in publications just the average statistics or are the weighted average or center statistics used? Attached are the stats of the problematic subjects. Any advice would be greatly appreciated! Emily ___ 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] DTI Statistics
Weighted average recommended, see my previous email. On Tue, 5 Aug 2014, Emily Louise Belleau wrote: Hello all, I was just wondering if in publications/papers it is more common to report the average FA statistics, the weighted average statistics, or the center statistics (the average of the highest probability pathway). These are the statistics provided by Tracula. Thanks, Emily ___ 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] Steps for Longitudinal trac-all
Hi Yoon - Sorry, the config file is necessary for anything that doesn't use default settings for trac-all, and that includes running it in longitudinal mode. What kind of cluster do you have? I'm working on making running trac-all easier on clusters that are not currently supported, as part of the 5.4 release. a.y On Tue, 12 Aug 2014, Chung, Yoonho wrote: Dear FS experts. I am trying run trac-all - the longitudinal version - on the cluster and not by using the dmrirc file. I am looking at the 'trac-all -help' and also the wiki, but I couldn't find a flag or option where I could specify the use of unbiased-template (e.g. [subjectID-base]) and other steps that may be necessary for the longitudinal analysis. Could someone please provide the steps that is required for running the longitudinal stream using 'trac-all' ? Thank you very much. Best, Yoon ___ 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] Cortical thickness via freesurfer
Dear all. I have a question concerning the estimation of cortical thickness in freesurfer. My overall goal is the comparison of a patient and matched control group with VBM and cortical thickness. My first try was the recon-all with masked MP2RAGE UNI-Images. Unfortunately it executed with error due to a not successfull skull-stripping Secondly I was going to skull-strip in AFNI and feed the skull-stripped image to the recon-all, but unfortunately the skull-stripping in AFNI was better but not as good as hoped. Next idea now is using the output of the VBM8 of SPM. Is it possible to use the segmented grey matter image from SPM in the recon-all to calculate overall cortical thickness and which steps of the recon-all are needed to be excluded for that? I am basically not interested in white matter...is it needed in the algorithm in general? The step 15 starts with the wm edits. So in case I am able to use only the segmented grey matter image from the VBM toolbox to avoid needing to skull-strip, I need to start with the step 21 (autorecon2-pial) of the recon-all? Or is there a possibility to improve the skull-stripping somehow? I tried lowering the threshold by adding the watershed trying to be more liberal, but it did not work as I was hoping... Thank you all so much in advance! Best Regards, Laura ___ 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] Checking in about FLAIR Registration Problem
Good morning, I wrote several weeks ago about a bbregister problem that we’ve encountered (I’ve attached the original email below). I’d like to check back in about the status of the patch that was being developed. Thank you for your time and assistance! Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzam...@illinois.edumailto:mzam...@illinois.edu 815-980-3882 This email is related to the archived “bbregister and FLAIR” email chain posted by Kayle Sawyer on 5/23/2014 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html). We have also been registering with FLAIR scans, and have run into a problem with approximately half of our subjects. Recon-all completes successfully but a bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve attached two screenshots, the first of which shows a bad registration and the second of which shows a good registration. Per your previous suggestion, we ran bbregister using the following flag: bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat --t2 --lta reg.test.lta This did result in a good registration, and we are hoping to incorporate this into our processing pipeline to ensure that we can use the FLAIR for refining the pill surface. The problem that we’ve run into is that we aren’t sure at which point this bbregister step occurs within the recon-all process flow. We were thinking there are a couple of possibilities: 1. manually create the transformation matrix for the FLAIR using the command mentioned above, and then re-run whichever steps necessary in recon-all to include this manually created xform; 2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with whatever steps/flags we need to include this FLAIR image to refine the pial surface. Unfortunately we're not exactly sure which flags to include in recon-all in order to most efficiently re-process our data with the manually created FLAIR transformation, and we were hoping you might offer some advice on this point. Please let me know if I can provide any additional information. [cid:795E512B-0727-4B3D-8B43-17BE1640FBD8@beckman.uiuc.edu][cid:9003C1C6-AA59-46E3-BF4A-0CEE22C57030@beckman.uiuc.edu] ___ 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] None region label number (color) not in FreeSurferColorLUT.txt
I am trying to make a custom label color scheme and wanted to change the None. Region but the FreeSurferColorLUT.txt only lists the unknown region (0) rather than None. I replaced the unknown region label name with None. to no avail like this. Is the None. region a different label number and color code? 0 None. 120 120 120 0 1 bankssts120 120 120 0 2 caudalanteriorcingulate 120 120 120 0 3 caudalmiddlefrontal 120 120 120 0 4 corpuscallosum 120 120 120 0 5 cuneus 120 120 120 0 6 entorhinal 120 120 120 0 7 fusiform120 120 120 0 8 inferiorparietal120 120 120 0 9 inferiortemporal120 120 120 0 10 isthmuscingulate120 120 120 0 11 lateraloccipital120 120 120 0 12 lateralorbitofrontal120 120 120 0 13 lingual 120 120 120 0 14 medialorbitofrontal 120 120 120 0 15 middletemporal 120 120 120 0 16 parahippocampal 120 120 120 0 17 paracentral 120 120 120 0 18 parsopercularis 120 120 120 0 19 parsorbitalis 120 120 120 0 20 parstriangularis120 120 120 0 21 pericalcarine 255 0 0 0 22 postcentral 120 120 120 0 23 posteriorcingulate 120 120 120 0 24 precentral 255 192 203 0 25 precuneus 120 120 120 0 26 rostralanteriorcingulate120 120 120 0 27 rostralmiddlefrontal255 99 710 28 superiorfrontal 120 120 120 0 29 superiorparietal240 128 128 0 30 superiortemporal120 120 120 0 31 supramarginal 120 120 120 0 32 frontalpole 120 120 120 0 33 temporalpole120 120 120 0 34 transversetemporal 255 69 00 35 insula 120 120 120 0 Eric Axelson Research Specialist Department of Psychiatry Iowa Neuroimaging Consortiumhttp://www.medicine.uiowa.edu/iowaneuroimagingconsortium/ University of Iowa 319-384-9206 eric-axel...@uiowa.edumailto:eric-axel...@uiowa.edu Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ 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] mismatch between FWHM data in fwhm.dat specified smoothing kernel
Dear Surfers, While running a mri_glmfit-sim (monte carlo simulation) for roi analyses generated using mri_glmfit, I encountered the following error code: ERROR: cannot find /Applications/MRI/freesurfer_5.30_x86_64/average/mult-comp-cor/fsaverage/lh/cortex/fwhm31/abs/th13/mc-z.csd I checked the fwh.dat file within my glm/ directories and realize that there is a discrepancy between the fwhm I set for the analyses and the fwhm in this file (which explains why I encountered the error above.) Can someone explain why there is a large discrepancy for these roi analyses (which is specified using the --label option)? What kinds of things can I do to run the monte carlo simulation appropriately? Thank you, Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health ___ 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] mismatch between FWHM data in fwhm.dat specified smoothing kernel
The fwhm.dat is computed from your data and reflects all the spatial correlation in your data, not just the smoothing you imposed. It is usually the case that there is some inherent smoothness and so the total smoothness is more than what you apply. This may be due to an outlier or just that some areas don't fit the GLM that well (which will create correlation). It could be that one or more subjects have a global thickness that tends to be less than the rest of the subjects. Some modalities (eg, gyrification) also tend to have very high inherent spatial correlation. doug On 8/18/14 11:42 AM, Vy Dinh wrote: Dear Surfers, While running a mri_glmfit-sim (monte carlo simulation) for roi analyses generated using mri_glmfit, I encountered the following error code: ERROR: cannot find /Applications/MRI/freesurfer_5.30_x86_64/average/mult-comp-cor/fsaverage/lh/cortex/fwhm31/abs/th13/mc-z.csd I checked the fwh.dat file within my glm/ directories and realize that there is a discrepancy between the fwhm I set for the analyses and the fwhm in this file (which explains why I encountered the error above.) Can someone explain why there is a large discrepancy for these roi analyses (which is specified using the --label option)? What kinds of things can I do to run the monte carlo simulation appropriately? Thank you, Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health ___ 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] FreeSurfer platform/performance questions
Hello FreeSurfer mailing list, First off, I am not a scientist and I have no experience running FreeSurfer. I have installed it, and seen it run, but that's it. I work for the IT department in the Beckman Institute, part of the University of Illinois. We support a computer lab here called the Visualization Laboratory - aka Vislab. (http://itg.beckman.illinois.edu/visualization_laboratory/) The Vislab lab has dozens of very nice workstations in it. (16 x 3GHz Xeon cores, 128GB of mem, NVIDIA Quadro K6000 video, etc.) In short, the Vislab supports research which needs high end computing. (less power than supercomputers, but much better than normal desktops and much easier to access/use than supercomputers) The Vislab has hundreds of active users, students, faculty, postdocs, etc., all of whom do some kind of scientific research. One of the packages we have recently installed upon request is FreeSurfer. We have installed freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz on our Red Hat Enterprise Linux 6 workstations, as well as on our Windows 7 Enterprise 64bit workstations. We have also installed Oracle's VirtualBox on a Windows 7 Enterprise 64bit machine, and run the VM freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz inside that virtual environment. The researchers who requested FreeSurfer are all part of the same group, and they are trying to complete a very large research project which requires FreeSurfer to process large amounts of data. They have normally been running FreeSurfer on the VM in the XUbuntu VirtualBox environment on their own average desktop PC's. However, they are concerned about their processing time with FreeSurfer, so they are hoping to take advantage of the Vislab computing resources to decrease the processing time in FreeSurfer. We are running into the following problems/concerns: 1) The FreeSurfer VM (Xubuntu) that runs in VirtualBox is a 32bit host. Is there a 64bit VM available? That 32bit host can only access 4GB of memory, whereas they would like to be able to access more of the workstations 128GB of memory. 2) The users have expressed concern about switching platforms to Red Hat Enterprise Linux6 with the FreeSurfer freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz installed. They have told us that FreeSurfer on XUbuntu might give different results than if it were run on Red Hat Enterprise Linux 6, given the same dataset. They are concerned about switching platforms in the middle of the research study, and that it might contaminate results. Is this possible? Or should the same version of FreeSurfer provide the same results, even with a different platform? 3) Does anyone else on this list run very large FreeSurfer processes on high end 64bit computers? If a high-end processing method works well for you, I would love to hear about it so I can share it with the researchers here. Thanks for your time! Alex Lazarevich 5321 Beckman Institute - 217-244-1565 Information Technology Services - http://its.beckman.illinois.eduhttp://its.beckman.illinois.edu/ Beckman Institute - http://beckman.illinois.eduhttp://beckman.illinois.edu/ University of Illinois - http://illinois.eduhttp://illinois.edu/ ___ 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 platform/performance questions
Nevermind question 2, I was just shown this from the FreeSurfer website: Important Note! When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms (for instance the 32b and 64b CentOS 4 builds should produce identical results), there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). But I'm still hoping for some advice on question 1 and 3. Thanks! Alex From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lazarevich, Alexander Sent: Monday, August 18, 2014 11:08 AM To: freesurfer@nmr.mgh.harvard.edu Cc: Taylor, Marc D Subject: [Freesurfer] FreeSurfer platform/performance questions Hello FreeSurfer mailing list, First off, I am not a scientist and I have no experience running FreeSurfer. I have installed it, and seen it run, but that's it. I work for the IT department in the Beckman Institute, part of the University of Illinois. We support a computer lab here called the Visualization Laboratory - aka Vislab. (http://itg.beckman.illinois.edu/visualization_laboratory/) The Vislab lab has dozens of very nice workstations in it. (16 x 3GHz Xeon cores, 128GB of mem, NVIDIA Quadro K6000 video, etc.) In short, the Vislab supports research which needs high end computing. (less power than supercomputers, but much better than normal desktops and much easier to access/use than supercomputers) The Vislab has hundreds of active users, students, faculty, postdocs, etc., all of whom do some kind of scientific research. One of the packages we have recently installed upon request is FreeSurfer. We have installed freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz on our Red Hat Enterprise Linux 6 workstations, as well as on our Windows 7 Enterprise 64bit workstations. We have also installed Oracle's VirtualBox on a Windows 7 Enterprise 64bit machine, and run the VM freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz inside that virtual environment. The researchers who requested FreeSurfer are all part of the same group, and they are trying to complete a very large research project which requires FreeSurfer to process large amounts of data. They have normally been running FreeSurfer on the VM in the XUbuntu VirtualBox environment on their own average desktop PC's. However, they are concerned about their processing time with FreeSurfer, so they are hoping to take advantage of the Vislab computing resources to decrease the processing time in FreeSurfer. We are running into the following problems/concerns: 1) The FreeSurfer VM (Xubuntu) that runs in VirtualBox is a 32bit host. Is there a 64bit VM available? That 32bit host can only access 4GB of memory, whereas they would like to be able to access more of the workstations 128GB of memory. 2) The users have expressed concern about switching platforms to Red Hat Enterprise Linux6 with the FreeSurfer freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz installed. They have told us that FreeSurfer on XUbuntu might give different results than if it were run on Red Hat Enterprise Linux 6, given the same dataset. They are concerned about switching platforms in the middle of the research study, and that it might contaminate results. Is this possible? Or should the same version of FreeSurfer provide the same results, even with a different platform? 3) Does anyone else on this list run very large FreeSurfer processes on high end 64bit computers? If a high-end processing method works well for you, I would love to hear about it so I can share it with the researchers here. Thanks for your time! Alex Lazarevich 5321 Beckman Institute - 217-244-1565 Information Technology Services - http://its.beckman.illinois.eduhttp://its.beckman.illinois.edu/ Beckman Institute - http://beckman.illinois.eduhttp://beckman.illinois.edu/ University of Illinois - http://illinois.eduhttp://illinois.edu/ ___ 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
[Freesurfer] download link broken?
Hi, Trying to download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Link gives 550 error and terminal error is: No such directory 'pub/dist/freesurfer/5.3.0' Please advise -- Wynn Legon PhD Assistant Professor Department of Physical Medicine and Rehabilitation School of Medicine University of Minnesota R398 - 426 Church St. E Minneapolis, MN 55455 USA Ph. (612) 626-1183 ___ 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] download link broken?
Hi Wynn - There is a scheduled outage of the Martinos Center storage cluster today and tomorrow. a.y On Mon, 18 Aug 2014, Wynn Legon wrote: Hi,Trying to download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Link gives 550 error and terminal error is: No such directory 'pub/dist/freesurfer/5.3.0' Please advise -- --- -Wynn Legon PhD Assistant Professor Department of Physical Medicine and Rehabilitation School of Medicine University of Minnesota R398 - 426 Church St. E Minneapolis, MN 55455 USA Ph. (612) 626-1183 ___ 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] no improvement for recon-all result after edits
Hi Freesurfer experts, I was doing some manual editing on our subjects which are patients with lesions. I managed to correct most of them, however, 4 subjects have the same problem that I can't fix no matter what edits I tried. So, the 4 subjects, they all have the same problem, which is: frontal part of superior temporal gyrus region is not segmented as white matter, thus they are just missing from the final surfaces and final segmentations. But when just do eye check, there is nothing wrong with this part, even the intensity looks the same of other white matter parts.Its just cut suddenly. When I went back to those subjects, first I tried with control points. - It didnt help. I confirmed that white matter is present connected to the main brain white matter volume. -- I reran from recon-all autorecon2-wm, didnt help. Then I checked the aseg.mgz, that part is segmented as white matter correctly. I even modified the aseg.mgz (although not suggested), it still didn't work It is just weird that the surface was just cut from the middle of STG. So, is there any other way I can tell FreeSurfer that this is really STG and please keep it? Thanks!! -- Regards, Jidan ___ 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.
