Freesurfer

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Re: [Freesurfer] Longitudinal TRACULA: mri_convert
by Vincent Koppelmans 30 Nov '16

30 Nov '16

Dear Anastasia, I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html) He mentioned that obtaining a new license could solve the issue. It did, so my problem is resolved. Best, Vincent ________________________________________ Dear Anastasia, I have checked the image and it looks good. I don't think the image is the problem, especially considering that my issue is also popping up with standard data. See for example the following code: $ echo $FREESURFER_HOME /home/mriuser/privatemodules/freesurfer $ cksum $(which mri_convert) 1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert $ echo $FSLDIR /home/mriuser/privatemodules/fsl $ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh mri_convert /home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz test.mgh $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz... crypt_gkey = (null) Segmentation fault (core dumped) The reason I am posting this with 'Longitudinal TRACULA' in the title is because I only have this issue with the mri_convert that is bundled with the TRACULA update (see my first post). The original mri_convert bundled with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert files. However, this version does not allow multiple frame numbers: Original frame options of mri_convert (FS v5.3.0 stable centos6 64) -f, --frame frameno keep only 0-based frame number Frame options of the updated mri_convert (tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz) -f, --frame frameno [...] keep only 0-based frame number(s) Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert --frame', which is why I need the updated version. Do you have any suggestions for me? Thank you! best, Vincent ________________________________________ Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA but probably something about the format of your input nifti volume. How did you create that volume? Can you open it in freeview and view it normally? a.y ________________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans [vkop...(a)umich.edu] Sent: Wednesday, November 30, 2016 1:33 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal TRACULA: mri_convert Hello Freesurfer experts, I am trying to run longitudinal TRACULA but I am getting an error early on in the process that seems to originate from mri_convert: #------------------------------------- /home/mriuser/privatemodules/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Nov 30 09:10:55 EST 2016 mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz Segmentation fault (core dumped) Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Some information about my setup: -------------------------------- *Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 *Freesurfer TRACULA update installed: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/t… *Linux version: CentOS Linux release 7.2.1511 (Core) centos-release-7-2.1511.el7.centos.2.10.x86_64 Is there a fix for this problem? Thanks! - Vincent

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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting
by Antonin Skoch 30 Nov '16

30 Nov '16

Dear experts, given sub-optimal results of my surfaces I referred to in my previous post, I have tested several different settings and input data preparation to obtain optimal pial surfaces in my modified HCP pipeline. I tested all variants in 5 representative subjects. My modified HCP pipeline uses FreeSurfer V6beta and full hires recon (-cm option) with 0.7mm3 data (including FreeSurferHiResWhite.sh and FreeSurferHiResPial.sh where effectively no up and downsampling is done since all steps are done in original 0.7 mm3 resolution). I have played with input data and parameters of 2nd pass mris_make_surfaces -T2pial in FreeSurferHiResPial.sh Since FreeSurferHiResPial.sh does not use aseg-informed and white surface-informed normalization and brain masking of T2 (which is default in recon-all), I also tested performance of this option (using commands borrowed from recon-all -T2pial). Since -nsigma_below 3 (default in FreeSurferHiResPial.sh) with combination of freeSurfer V6beta version of mris_make_surfaces cuts out some portions of gray matter in my data (in contrast to FreeSurfer 5.3 version where it seems that nsigma_below 3 suffices!), I increased -nsigma_below to 5 (which is default value used in recon-all -T2pial). My tested versions were following: For modified full hires HCP pipeline with FreeSurfer V6beta: 1. -nsigma_below 3 (original FreeSurferHiResPial.sh) 2. -nsigma_below 5 3. -nsigma_below 5 with additional masking of T2 by brainmask.mgz 4. -nsigma_below 5 with aseg-informed normalization of T2 (using mri_normalize) 5. -nsigma_below 5 with aseg-informed normalization of T2 (using mri_normalize) and masking of T2 by brainmask.mgz And, as Matt suggested, I also tried: 6. standard FreeSurfer V6 beta recon-all -pial and -T2pial (apart from standard recon-all I used as ?h.white input the output of FreeSurferHiResWhite.sh , but I think it should not matter in this context). My observations are following: It is definitely needed to increase -nsigma_below from 3 due to significant cut out of portions of gray matter in some regions, in some subjects these regions are very large. Increase nsigma_below to 5 prevents cutting out of gray matter, however it leads to leak of surfaces to cerebellum (as I showed in my previous post) for all my versions (to varying extent). I am not sure how much significant the extend of error is, looking subjective it seems significant, but accounting the fact that the data is of high resolution, the maximal error would be approx. 2 mm. -nsigma_below 5 with aseg-informed normalization does not work well in some areas and results in cutting out gray matter in some regions (but not to such great extend as in nsigma_below 3) FreeSurfer V6beta tends in some (not very large) areas to cut out gray matter. On the other hand, in some areas and in some subjects it produces largest leak of surfaces to dura and cerebellum from all my tested versions. mri_normalize of T2 has in some regions sub-optimal performance on pial surface estimation and actually performs worse than global (no aseg-informed and no white surface-informed) normalization ( especially at temporal poles, but also in some areas at convexity). I have indecisive results with masking. In some subjects it had almost no effect, in one subject it definitely improved the leak to dura, but in some subjects the results were quite opposite. I am not sure why the masking should matter since the mask is larger than the regions where the surfaces are extending, but I am not very familiar with internals of mris_make_surfaces (the masked T2 maybe after internal smoothing in mris_make_surfaces can propagate the voxel values even to regions relevant for surface estimation). Therefore I would tend to use the masking. Overall best results (better than with V6beta recon-all) I obtained with -nsigma_below 5 with global (no aseg-informed and white surface-informed) normalization of T2 as it is done in FreeSurferHiResPial.sh. My overall impresion: I was quite frustrated to observe, how much the results are dependent on particular setting of the parameters and input data. But maybe my expectations of accuracy of surfaces were unrealistically high.... Regards, Antonin

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Longitudinal TRACULA: mri_convert
by Vincent Koppelmans 30 Nov '16

30 Nov '16

Hello Freesurfer experts, I am trying to run longitudinal TRACULA but I am getting an error early on in the process that seems to originate from mri_convert: #------------------------------------- /home/mriuser/privatemodules/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Nov 30 09:10:55 EST 2016 mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz Segmentation fault (core dumped) Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Some information about my setup: -------------------------------- *Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 *Freesurfer TRACULA update installed: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/t… *Linux version: CentOS Linux release 7.2.1511 (Core) centos-release-7-2.1511.el7.centos.2.10.x86_64 Is there a fix for this problem? Thanks! - Vincent

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ERROR: cannot find RB_all_2008-03-26.gca
by Douglas Merkitch 30 Nov '16

30 Nov '16

Hello experts, I was attempting to test out the freesurfer v6 beta and encountered the following error during dicom conversion: "ERROR: cannot find /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca". I'm currently running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5. Any help would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.
by Knut J Bjuland 30 Nov '16

30 Nov '16

Hi, I would like to to obtain FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a DWI file, either produced by dt_recon (or perhaps better - from Tracula) and an anatomy file in atlas space and then use WMParcStatsLUT.txt or FreeSurferColorLUT.txt (not sure which) to obtain the wm ROIs containing FA data. And then register the aparc+aseg.mgz to the FA image and use mri_segstats to retrieve FA data from the white matter ROIs. I have done this: # Register DTI file to individual anatomy space 1) dt_recon --i 1/dti/1.dcm --s 001 --b 1/dti/bval 1/dti/bvec --o 1/dtrecon # Register fa.nii to wmparc.mgz and aparc+aseg.mgz 2) mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/wmparc.mgz --inv --interp nearest --o 1/mri/aseg2DTI.mgz --no-save-reg mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/aparc+aseg.mgz --inv --interp nearest --o 1/mri/aparc-aseg2DTI.mgz --no-save-reg 3) It works for wmparc, in that I get data that range from 0.0 to 0.4 with mean = 0.04 (which is a little low for FA values): mri_segstats --seg 1/mri/wmparc2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal But for aparc+aseg, it doesn't produce any data: mri_segstats --seg 1/mri/aparc-aseg2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal output: Found 1 segmentations Computing statistics for each segmentation 0 3014 wm-lh-medialorbitofrontal 0 0.000 Reporting on 0 segmentations mri_segstats done Questions: 1) Am I right to use FreeSurferColorLUT.txt and not WMParcStatsLUT.txt? 2) In order to get FA data from the wm regions corresponding to cortical ROIs, should I use the FA registrated to wmparc.mgz or aparc+aseg.mgz? 3) If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii? sincerely yours, Knut Jørgen Bjuland PhD

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Re: [Freesurfer] recon-all -autorecon2 error.
by miracle ozzoude 29 Nov '16

29 Nov '16

Hello Doug and Bruce, I ran the script and it worked however, volumes did not align on freeview.* Here's the mri_info for orig.mgz: * Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -110.0032 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 110.0032 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 91.0000 talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_ 120223/fsdir3/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 17.9968 0.0000 0.0000 1.0000 -17.9968 0.0000 -1.0000 0.0000 219.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 17.9968 -0.0000 -0.0000 -1.0000 219.0000 -0.0000 1.0000 -0.0000 17.9968 -0.0000 -0.0000 -0.0000 1.0000 *Here's the mri_info for brainmask.mgz after including -rl orig.mgz* Volume information for brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -110.0032 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 110.0032 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 91.0000 talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_ 120223/fsdir3/mri/transforms/talairach.xfm Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 17.9968 0.0000 1.0000 0.0000 -17.9968 0.0000 0.0000 1.0000 -37.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 17.9968 -0.0000 1.0000 -0.0000 17.9968 -0.0000 -0.0000 1.0000 37.0000 -0.0000 -0.0000 -0.0000 1.0000 I sent the orig.mgz, brainmask.mgz (my stripped volume from lesion explorer that i converted to mgz) and the HfBd.img/hdr (stripped volume in analyze format which I used to convert to mgz) to the freesurfer file drop (subject = recon-all -autorecon2 error Paul) https://gate.nmr.mgh.harvard.edu/filedrop2/index.php Please can you inspect to see why both images (orig.mgz and brainmask.mgz) do not align and cannot finish recon-all -autorecon2? THANK YOU VERY MUCH Paul On Tue, Nov 29, 2016 at 3:20 PM, miracle ozzoude <miracooloz(a)gmail.com> wrote: > Hello Doug and Bruce, > > I ran the script and it worked however, volumes did not align on freeview.* > Here's the mri_info for orig.mgz: * > Volume information for orig.mgz > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.000000, 1.000000, 1.000000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees > nframes: 1 > PhEncDir: UNKNOWN > FieldStrength: 0.000000 > ras xform present > xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = > -110.0032 > : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = > 110.0032 > : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = > 91.0000 > > talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_ > 120223/fsdir3/mri/transforms/talairach.xfm > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: > -1.0000 0.0000 0.0000 17.9968 > 0.0000 0.0000 1.0000 -17.9968 > 0.0000 -1.0000 0.0000 219.0000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant -1 > > ras to voxel transform: > -1.0000 -0.0000 -0.0000 17.9968 > -0.0000 -0.0000 -1.0000 219.0000 > -0.0000 1.0000 -0.0000 17.9968 > -0.0000 -0.0000 -0.0000 1.0000 > *Here's the mri_info for brainmask.mgz after including -rl orig.mgz* > Volume information for brainmask.mgz > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.000000, 1.000000, 1.000000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: > 0.00 degrees > nframes: 1 > PhEncDir: UNKNOWN > FieldStrength: 0.000000 > ras xform present > xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = > -110.0032 > : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = > 110.0032 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = > 91.0000 > > talairach xfm : /net/synapse/nt/mozzoude/processing/freesurfer/176_001_ > 120223/fsdir3/mri/transforms/talairach.xfm > Orientation : LAS > Primary Slice Direction: axial > > voxel to ras transform: > -1.0000 0.0000 0.0000 17.9968 > 0.0000 1.0000 0.0000 -17.9968 > 0.0000 0.0000 1.0000 -37.0000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant -1 > > ras to voxel transform: > -1.0000 -0.0000 -0.0000 17.9968 > -0.0000 1.0000 -0.0000 17.9968 > -0.0000 -0.0000 1.0000 37.0000 > -0.0000 -0.0000 -0.0000 1.0000 > > I have attached the orig.mgz, brainmask.mgz (my stripped volume from > lesion explorer that i converted to mgz) and the HfBd.img/hdr (stripped > volume in analyze format which I used to convert to mgz). Please can you > inspect to see why both images (orig.mgz and brainmask.mgz) do not align. > > THANK YOU VERY MUCH > Paul > > On Tue, Nov 29, 2016 at 1:58 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> yes, though you should not need to spec the output orientation >> (redundant) or the in_type (it can figure that out) >> >> >> On 11/29/2016 01:46 PM, miracle ozzoude wrote: >> > Thanks bruce and doug. The orientation is wrong hence, why I am using >> > the orientation string. But, the above script is correct? >> > >> > On Tue, Nov 29, 2016 at 1:39 PM, Douglas N Greve >> > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> > >> > don't use the orientation strings unless the orientation is wrong >> > >> > >> > On 11/29/2016 01:38 PM, Bruce Fischl wrote: >> > > you may not need the out_orientation, but perhaps someone else >> > knows? >> > > On Tue, 29 Nov 2016, miracle ozzoude wrote: >> > > >> > >> Hello Bruce, >> > >> I wanted to confirm if this is the right script when converting >> > from >> > >> one format to another using mri_convert (if i want to use >> > >> orig.mgz as template volume): >> > >> mri_convert --in_type analyze --in_orientation LAS -rl orig.mgz >> > >> --out_type mgz --out_orientation LAS brainmask.img brainmask.mgz >> > >> Thanks, >> > >> Paul >> > >> >> > >> On Mon, Nov 28, 2016 at 7:15 PM, <miracooloz(a)gmail.com >> > <mailto:miracooloz@gmail.com>> wrote: >> > >> Awesome. Thank you very much Bruce. >> > >> >> > >> Sent from my BlackBerry 10 smartphone. >> > >> Original Message >> > >> From: Bruce Fischl >> > >> Sent: Monday, November 28, 2016 5:14 PM >> > >> To: Freesurfer support list >> > >> Reply To: Freesurfer support list >> > >> Subject: Re: [Freesurfer] recon-all -autorecon2 error. >> > >> >> > >> -rl is for "reslice like" and you include it in the >> > mri_convert >> > >> command >> > >> line with orig.mgz as the template volume. Run mri_convert >> > >> --help and it >> > >> should be clear >> > >> >> > >> Bruce >> > >> >> > >> >> > >> On Mon, 28 >> > >> Nov 2016, miracooloz(a)gmail.com >> > <mailto:miracooloz@gmail.com> wrote: >> > >> >> > >> > Thanks a lot Bruce. What do you mean by -rl and how do I >> > >> incorporate it to mri_convert? >> > >> > Best, >> > >> > Paul >> > >> > >> > >> > Sent from my BlackBerry 10 smartphone. >> > >> > Original Message >> > >> > From: Bruce Fischl >> > >> > Sent: Monday, November 28, 2016 4:57 PM >> > >> > To: Freesurfer support list >> > >> > Reply To: Freesurfer support list >> > >> > Subject: Re: [Freesurfer] recon-all -autorecon2 error. >> > >> > >> > >> > I think this is your problem - the brainmask is not in >> the >> > >> same voxel >> > >> > coords as the other volumes. YOu probably need to -rl >> > >> orig.mgz in your >> > >> > conversion, then make sure that the volumes look aligned >> in >> > >> freeview (and >> > >> > that mri_info gives the same ras2vox and such for them) >> > >> > On Mon, 28 Nov 2016, >> > >> > miracle ozzoude wrote: >> > >> > >> > >> >> Oh. Thanks bruce. For mri_info for my orig.mgz is >> > >> >> Volume information for orig.mgz >> > >> >> type: MGH >> > >> >> dimensions: 256 x 256 x 256 >> > >> >> voxel sizes: 1.000000, 1.000000, 1.000000 >> > >> >> type: UCHAR (0) >> > >> >> fov: 256.000 >> > >> >> dof: 0 >> > >> >> xstart: -128.0, xend: 128.0 >> > >> >> ystart: -128.0, yend: 128.0 >> > >> >> zstart: -128.0, zend: 128.0 >> > >> >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, >> > >> flip angle: 0.00 degrees >> > >> >> nframes: 1 >> > >> >> PhEncDir: UNKNOWN >> > >> >> FieldStrength: 0.000000 >> > >> >> ras xform present >> > >> >> xform info: x_r = -1.0000, y_r = 0.0000, z_r = >> > >> 0.0000, c_r = -110.0032 >> > >> >> : x_a = 0.0000, y_a = 0.0000, z_a = >> > >> 1.0000, c_a = 110.0032 >> > >> >> : x_s = 0.0000, y_s = -1.0000, z_s = >> > >> 0.0000, c_s = 91.0000 >> > >> >> >> > >> >> talairach xfm >> > >> >> > :/net/synapse/nt/mozzoude/processing/freesurfer/176_001_120 >> 223/fsdir1/mri/transforms/tala >> > >> >> irach.xfm >> > >> >> Orientation : LIA >> > >> >> Primary Slice Direction: coronal >> > >> >> >> > >> >> voxel to ras transform: >> > >> >> -1.0000 0.0000 0.0000 17.9968 >> > >> >> 0.0000 0.0000 1.0000 -17.9968 >> > >> >> 0.0000 -1.0000 0.0000 219.0000 >> > >> >> 0.0000 0.0000 0.0000 1.0000 >> > >> >> >> > >> >> voxel-to-ras determinant -1 >> > >> >> >> > >> >> ras to voxel transform: >> > >> >> -1.0000 -0.0000 -0.0000 17.9968 >> > >> >> -0.0000 -0.0000 -1.0000 219.0000 >> > >> >> -0.0000 1.0000 -0.0000 17.9968 >> > >> >> -0.0000 -0.0000 -0.0000 1.0000 >> > >> >> >> > >> >> Here's the mri_info for my new brainmask.mgz: >> > >> >> Volume information for brainmask.mgz >> > >> >> type: MGH >> > >> >> dimensions: 256 x 256 x 182 >> > >> >> voxel sizes: 0.859400, 0.859400, 1.000000 >> > >> >> type: UCHAR (0) >> > >> >> fov: 220.006 >> > >> >> dof: 0 >> > >> >> xstart: -110.0, xend: 110.0 >> > >> >> ystart: -110.0, yend: 110.0 >> > >> >> zstart: -91.0, zend: 91.0 >> > >> >> TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 >> > msec, >> > >> flip angle: 0.00 degrees >> > >> >> nframes: 1 >> > >> >> PhEncDir: UNKNOWN >> > >> >> FieldStrength: 0.000000 >> > >> >> ras xform present >> > >> >> xform info: x_r = -1.0000, y_r = 0.0000, z_r = >> > >> 0.0000, c_r = 0.0000 >> > >> >> : x_a = 0.0000, y_a = 1.0000, z_a = >> > >> 0.0000, c_a = 0.0000 >> > >> >> : x_s = 0.0000, y_s = 0.0000, z_s = >> > >> 1.0000, c_s = 0.0000 >> > >> >> >> > >> >> talairach xfm : >> > >> >> Orientation : LAS >> > >> >> Primary Slice Direction: axial >> > >> >> >> > >> >> voxel to ras transform: >> > >> >> -0.8594 0.0000 0.0000 110.0032 >> > >> >> 0.0000 0.8594 0.0000 -110.0032 >> > >> >> 0.0000 0.0000 1.0000 -91.0000 >> > >> >> 0.0000 0.0000 0.0000 1.0000 >> > >> >> >> > >> >> voxel-to-ras determinant -0.738568 >> > >> >> >> > >> >> ras to voxel transform: >> > >> >> -1.1636 -0.0000 -0.0000 128.0000 >> > >> >> -0.0000 1.1636 -0.0000 128.0000 >> > >> >> -0.0000 -0.0000 1.0000 91.0000 >> > >> >> -0.0000 -0.0000 -0.0000 1.0000 >> > >> >> >> > >> >> >> > >> >> On Mon, Nov 28, 2016 at 4:29 PM, Bruce Fischl >> > >> <fischl(a)nmr.mgh.harvard.edu >> > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> > >> >> Hi Paul >> > >> >> >> > >> >> if you run mri_info on the orig.mgz and your new >> > >> brainmask.mgz they should >> > >> >> give you the same thing in terms of ras2vox and such >> > >> >> cheers >> > >> >> Bruce >> > >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> > >> >> >> > >> >> This was the info from mri_convert when i converted >> > my skull >> > >> >> stripped volume to mgz >> > >> >> before replacing it with the brainmask from FS >> > >> >> mri_convert --in_type analyze --in_orientation LAS >> > >> --out_type mgz >> > >> >> --out_orientation LAS >> > >> >> brainmask.img brainmask.mgz >> > >> >> cp foldername/subjid/brainmask.mgz >> > >> >> foldername/subjd/mri/brainmask.mgz >> > >> >> >> > >> >> INFO: could not find ...mat file for direction cosine >> > >> infoINFO: >> > >> >> use ANALYZE 7.5 hdr -> >> > >> >> hist.orient value: 0, transverse unflipped (default >> > >> >> INFO : if not valid, please provide the information >> > ....... >> > >> .mat >> > >> >> file >> > >> >> analyzeRead() roi_scale 0.00000000 >> > >> >> TR= 1000.00, TE = 0.00, TI = 0.00, flip angle = 0.00 >> > >> >> setting input orientation to LAS >> > >> >> i_ras = (-1, 0, 0) >> > >> >> j_ras = (0,1,0) >> > >> >> k_ras = (0,0,1) >> > >> >> setting output orientation to LAS >> > >> >> writing to brainmask.mgz >> > >> >> >> > >> >> why do i need the orig.mgz? I thought I only had to >> > replace the >> > >> >> brainmask.mgz (from FS) >> > >> >> with mine brainmask,mgz( from lesion explorer after i >> have >> > >> >> renamed it to brainmask.mgz). >> > >> >> Also, I didn't use the "noskullstrip" flag like you >> > suggested. >> > >> >> Best, >> > >> >> paul >> > >> >> >> > >> >> On Mon, Nov 28, 2016 at 3:50 PM, Bruce Fischl >> > >> >> <fischl(a)nmr.mgh.harvard.edu >> > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> > >> >> I mean after you have converted it >> > >> >> On Mon, 28 Nov 2016, miracle ozzoude wrote: >> > >> >> >> > >> >> Thanks Bruce for the response. mri_info? >> > do you >> > >> mean >> > >> >> when i >> > >> >> converted it from analyze to >> > >> >> mgz or when I ran recon-all autorecon2 after >> > >> >> inserting it to >> > >> >> freesurfer. >> > >> >> >> > >> >> On Mon, Nov 28, 2016 at 3:09 PM, Bruce >> Fischl >> > >> >> <fischl(a)nmr.mgh.harvard.edu >> > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> > >> >> what is the output of mri_info on >> > your new >> > >> >> brainmask.mgz >> > >> >> and on say the >> > >> >> orig.mgz? You may need to conform you >> > >> brainmask >> > >> >> >> > >> >> On Mon, 28 Nov 2016, miracle ozzoude >> > wrote: >> > >> >> >> > >> >> Hello Freesurfer, I ran >> recon-all >> > >> >> -autorecon 1 -s >> > >> >> subjID on T1 >> > >> >> (T1_nii) image and after >> > >> >> that, I replaced the skull >> > stripped >> > >> >> volume generated >> > >> >> from FS with >> > >> >> the skull stripped >> > >> >> volume from lesion explorer ( >> > using >> > >> >> mri_convert >> > >> >> in_type analyze >> > >> >> in_orientation LAS >> > >> >> out-type img out_orientation LAS >> > >> mgz; cp >> > >> >> folder/brainmask.mgz >> > >> >> folder/subjID/mri/brainmask.mgz). Then, I >> > >> >> ran >> > >> >> recon-all >> > >> >> -autorecon2 -autorecon2 -s >> > >> >> subjID. My recon-all is stucked >> at >> > >> >> >> > >> >> CORRECTION DEFECT 0 (vertices=49378, >> > >> >> convex >> > >> >> hull=3422, v0 =0) >> > >> >> XL defect detected.... >> > >> >> >> > >> >> Please how do I resolve this >> > problem? >> > >> >> >> > >> >> I am running freesurfer-6 >> > >> development. I >> > >> >> have >> > >> >> attached the >> > >> >> recon-all/recon-all status to >> > >> >> the email. >> > >> >> >> > >> >> Thank you very much >> > >> >> >> > >> >> >> > >> >> _______________________________________________ >> > >> >> Freesurfer mailing list >> > >> >> Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> > >> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <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 >> > <http://www.partners.org/complianceline> . If the >> > >> >> e-mail was sent >> > >> >> to you in error >> > >> >> but does not contain patient information, >> > please >> > >> >> contact the >> > >> >> sender and properly >> > >> >> dispose of the e-mail. >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> _______________________________________________ >> > >> >> Freesurfer mailing list >> > >> >> Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <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 >> > <http://www.partners.org/complianceline> . If the e-mail was sent >> > >> >> to you in error >> > >> >> but does not contain patient information, please >> > contact the >> > >> >> sender and properly >> > >> >> dispose of the e-mail. >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> _______________________________________________ >> > >> >> Freesurfer mailing list >> > >> >> Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <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 >> > <http://www.partners.org/complianceline> . If the e-mail was >> > >> sent to you in error >> > >> >> but does not contain patient information, please >> > contact the >> > >> sender and properly >> > >> >> dispose of the e-mail. >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> > >> > >> > _______________________________________________ >> > >> > Freesurfer mailing list >> > >> > Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >> > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > >> > >> > >> > >> > >> >> > >> >> > >> >> > >> >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer(a)nmr.mgh.harvard.edu >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > <https://gate.nmr.mgh.harvard.edu/filedrop2> >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing: >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har >> vard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >

1 0

TRACULA Error in virtualbox
by Alexander Zent 29 Nov '16

29 Nov '16

I am trying to run TRACULA and keep getting the error FSLDIR: Undefined Variable. I have looked at the answers to this question that have been previously posted but cannot seem to remedy this problem. I'm running freesurfer 5.3 via virtualbox on windows. I have applied for a license and added that to the license.txt file but to no avail. Thank you and I look forward to hearing from you. Thanks, Alex

3 2

Using mri_glmfit to generate R (correlation) maps
by Morenikeji Adebayo 29 Nov '16

29 Nov '16

Hello Freesurfers, I'm interested in creating a group map where each vertex represents the correlation (as a correlation coefficient) between a task-related BOLD contrast value (ces.nii.gz) and a single covariate. This is analogous to a cortical thickness GLM with one group and one covariate, but I'd want an r-map instead of a sig-map. How might I accomplish this? It appears that mri_glmfit generates sig-maps, gamma-maps, etc, but not r-maps. Thanks in advance, Keji

2 8

recon-all -autorecon2 error.
by miracle ozzoude 29 Nov '16

29 Nov '16

Hello Freesurfer, I ran recon-all -autorecon 1 -s subjID on T1 (T1_nii) image and after that, I replaced the skull stripped volume generated from FS with the skull stripped volume from lesion explorer ( using mri_convert in_type analyze in_orientation LAS out-type img out_orientation LAS mgz; cp folder/brainmask.mgz folder/subjID/mri/brainmask.mgz). Then, I ran recon-all -autorecon2 -autorecon2 -s subjID. My recon-all is stucked at CORRECTION DEFECT 0 (vertices=49378, convex hull=3422, v0 =0) XL defect detected.... Please how do I resolve this problem? I am running freesurfer-6 development. I have attached the recon-all/recon-all status to the email. Thank you very much

4 15

Request for patch for mri_convert, nifti1Read(): unsupported slice timing pattern 5 error
by Jennifer Barredo 29 Nov '16

29 Nov '16

Hello Freesurfer experts, I'm trying to run the TRACULA preprocessing pipeline using data in NIFTI-1 format, but am receiving the following error: "nifti1Read(): unsupported slice timing pattern 5" Several other users have run into this problem. In the archives, there are a few links to dead file transfer protocols for a patch for mri_convert that might solve my problem. May I please have a patch for mri_convert? I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and OSX Yosemite. Thank you, Jennifer -- Jennifer Barredo, PhD Staff Scientist Providence VA Medical Center Research Affiliate Brown Institute for Brain Sciences jlbarredo(a)gmail.com Jennifer.Barredo(a)va.gov

1 0

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