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FLASH and MPRAGE sequences for segmentation on a GE 3.0T
by Sherwood, Matt 20 Jun '14

20 Jun '14

Freesurfer, We recently gained access to a new GE Discovery MR750w 3.0T GEM MRI with a 24 channel headcoil. Because this system is located at a nearby hospital and is used clinically, we do not have a research agreement with GE in place and, therefore, cannot edit the default pulse sequences. We were wondering what scans/parameters would give us optimal segmentation (similar to MPRAGE and/or FLASH at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&…) Thanks, Matthew Sherwood Medical Research Engineer Wright State Research Institute 4035 Colonel Glenn Hwy. Dayton, OH 45431 PH: 937.705.1025 FAX: 937.705.1095 EMAIL: matt.sherwood(a)wright.edu<mailto:matt.sherwood@wright.edu>

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Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain
by Paul Beach 20 Jun '14

20 Jun '14

Thomas, Thank you so much for this input. I tried out both the striatum and the general MNI152 template. For the striatum the match is *SO* much better. The MNI152 template also looks alright - though it's a little fuzzy. I'm pretty happy with this now and I'll definitely have more confidence in any striatum-based connectivity differences I see now. Thanks again. Paul On Thu, Jun 19, 2014 at 11:07 AM, Thomas Yeo <thomas.yeo(a)nus.edu.sg> wrote: > Sorry for the slow reply. Here's a (non-ideal) suggestion: > > 1) Assuming you are quite happy with the freesurfer striatal parcellation > in your AD subjects, then I am assuming freesurfer nonlinear registration > (talairach.m3z) is working quite well. Talairach.m3z warps your subject to > an internal freesurfer space (kinda like MNI305, but not quite). Let's say > the freesurfer recon-all output is at <something>/AD_SUBJECT_FS/ > > 2) Run the MNI152 1mm template (the one from FSL) through recon-all. > Recon-all will give you a Talairach.m3z that allows you to map the MNI152 > 1mm template to the internal freesurfer space. Let's say the freesurfer > recon-all output is at <something>/MNI152_FS/ > > 3) Then do the following: > > a) Use mri_vol2vol to upsample the Choi striatal atlas which is 2mm > resolution to the 1mm MNI152 template: > > >> mri_vol2vol --mov Choi_atlas.nii.gz --targ MNI152/mri/norm.mgz > --regheader --o Choi_atlas1mm.nii.gz --no-save-reg --interp nearest > > Notice that I use norm.mgz of the MNI template rather than the original > MNI template? norm.mgz is the 256 x 256 x 256 conformed version of the MNI > template that recon-all puts through. > > b) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space: > > >> setenv SUBJECTS_DIR <something> > >> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ > $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o > Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest > > c) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject: > > >> setenv SUBJECTS_DIR <something> > >> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s > AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z > talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph > > > This is not optimal because of the double interpolation. You might want to > use the MNI template instead of the Choi_atlas to test the above, so you > can check the goodness of the warp. The final warped MNI template should > hopefully look identical to your AD subject. If that works, then use the > Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z > below version 5, so you should use version 5x mri_vol2vol. > > --Thomas > > > > > > > > > > On Wed, Jun 18, 2014 at 10:04 PM, Harms, Michael <mharms(a)wustl.edu> wrote: > >> >> Hi, >> The recon-all based striatal parcellations are based on the anatomy of >> each particular subject, guided by a probabilistic atlas. That is >> inherently likely to be more accurate that just taking a set of >> ROIs/parcellations defined in some (non-probabilistic) atlas and warping >> them to each subject via an affine transformation, which is what it sounds >> like you are doing with the "Choi ROIs". >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> ----------------------------------------------------------- >> Conte Center for the Neuroscience of Mental Disorders >> Washington University School of Medicine >> Department of Psychiatry, Box 8134 >> 660 South Euclid Ave. Tel: 314-747-6173 >> St. Louis, MO 63110 Email: mharms(a)wustl.edu >> >> From: Paul Beach <pabeach1(a)gmail.com> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Wednesday, June 18, 2014 8:52 AM >> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Cc: Thomas Yeo <thomas.yeo(a)nus.edu.sg>, "Yeo, Boon Thye Thomas -- Boon >> Thye Thomas Yeo" <ythomas(a)csail.mit.edu> >> Subject: Re: [Freesurfer] Fwd: Improving translation of Choi striatal >> ROIs to original domain >> >> Hi Bruce, >> >> Thanks for the response. >> >> I actually got this pipeline partly from Thomas a few months back. >> However, I wasn't sure if anyone had suggestions perhaps for a recon-all >> based command for going from the MNI152 1mm template-based fit to >> individual subjects. The recon-all/Freesurfer inherent striatal >> parcellations are so well fitted to even my severe AD patients, so I was >> hoping I could somehow adapt this to the Choi ROIs. >> >> >> On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > wrote: >> >>> Hi Paul >>> >>> Thomas Yeo (ccd) would be the best person to help you, but he may not be >>> reading email for a while.... >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Wed, 18 Jun 2014, Paul Beach wrote: >>> >>> Hi Freesurfers, >>>> My processing stream involves moving the parcellated functional >>>> networks of >>>> Yeo and Choi to original subject domain to do connectivity analyses. >>>> While >>>> my process works very well for the Yeo networks I'm rather unsatisfied >>>> by >>>> the results of the Choi translations. >>>> >>>> I'm hoping someone has some suggestions for improving things so that the >>>> Choi ROIs map onto individual subjects nearly as well as the general >>>> Freesurfer striatal segmentations. >>>> >>>> NB - I work with AD patients, so I'm sure part of the problem is >>>> atrophy-based. However, I'm sure there are ways to improve things... >>>> >>>> My current pipeline involves two steps: >>>> mri_vol2vol \ >>>> --mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz >>>> \ >>>> --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \ >>>> --o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg >>>> --interp >>>> nearest >>>> >>>> mri_label2vol \ >>>> --seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \ >>>> --reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \ >>>> --invertmtx \ >>>> --o Choi_17Network_tight_striatum_orig.nii.gz \ >>>> --temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz >>>> >>>> I suspect one way to improve things would be to do a recon-all based >>>> procedure, but I have no clue what commands within the recon-all domain >>>> that >>>> would involve. >>>> >>>> >>>> Thanks for your suggestions. >>>> -- >>>> Paul Beach >>>> DO/PhD candidate - Year VI >>>> Michigan State University >>>> - College of Osteopathic Medicine >>>> - Neuroscience Program - MSU Cognitive and Geriatric Neurology Team >>>> (CoGeNT) >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >> >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program >> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) >> >> >> ------------------------------ >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

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Reducing Used Disk Space?
by Jamie Hanson 20 Jun '14

20 Jun '14

Hi Freesurfer List, Do folks have any recommendations on reducing the amount of space used by each subject? I looked a bit in the list archives but didn't see any recent tips. I had a large potential sample size (n=~750) and didn't know if I would have the estimated 375GBs processing would require. It looked as though there was potentially some space to trim (i.e., deleting some files in the mdi directory like nu.mgz, nu_noneck.mgz) once processing had completed). I wondered if anyone had a more exhaustive list (or suggestions) regarding files that could be deleted? Any help is greatly appreciated! Thanks much! Best, jamie. -- Jamie L. Hanson Postdoctoral Fellow, Laboratory of NeuroGenetics Duke University 417 Chapel Drive Duke West Campus Sociology-Psychology Building, Room 07A Durham, NC 27710 Email: jamielarshanson(a)gmail.com Website: http://jamiehanson.org/

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Monte Carlo correction
by Johnson, Eileanoir 20 Jun '14

20 Jun '14

Hi there, I am trying to run a monte carlo correction on my average subject, using the full mri-mcsim run with 10000 iterations (and about 200 participants). This is taking a long time, and the cluster I have access to has a limit of 72 hours which isn't long enough to finish processing. Is there a way to cut down on this processing time, i.e. cutting down on the iterations etc? Many thanks, Eileanoir

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mri_label2label results
by Yang, Daniel 20 Jun '14

20 Jun '14

Dear all, I found that mri_label2label generates different results, depending on whether the software’s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel

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Problem with freeview
by Bernardoni, Fabio 20 Jun '14

20 Jun '14

Dear all, trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell: ~>tcsh ~>source $FREESURFER_HOME/SetUpFreeSurfer.csh ~>setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~>cd $SUBJECTS_DIR ~>freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information. 1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64 Could anybody please telle me what's my problem? Thanks Fabio

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Can some send me rh.average.curvature.filled.buckner40.tif file
by Venkateswaran Rajagopalan 20 Jun '14

20 Jun '14

Dear All, when I run recon-all I encounter errro saying that rh.average.curvature.filled.buckner40.tif file is missing. I found this file missing in my average folder so if someone can send it as an attachment or guide me to where I can find it it will be great help. Many thanks in advance Venkat

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Control Points ignored
by Victor Kovac 19 Jun '14

19 Jun '14

Hello, I have run recon-all on two timepoints of a subject (MPS1011-4 and MPS1011-5). I added control points to MPS1011-4 after the initial recon-all processing because large areas of white matter were excluded. Unfortunately, ~50% of the control points I added were apparently ignored, as they did not cause the missed wm areas to be segmented (see attached images). I have run into this problem in a few other subjects as well, where large wm areas are missed even after adding control points and running recon-all -autorecon2-cp -autorecon3 The other timepoint exited with errors, leaving the brain unsegmented. Any advice on how to accurately analyze these timepoints would be greatly appreciated. Their recon-all logs are also attached. Thank you! Victor

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Decimate surface during recon-all
by Kai Schlamp 19 Jun '14

19 Jun '14

Hello again. I am still trying to project a label on a decimated surface. I tried to decimate the appropriate surface after recon-all and then to create a new label for this decimated surface, but this doesn't seem to work (see here <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36473.html>, unfortunately no answer yet). Is there a way to customize the recon-all pipeline, so that every surface that is generated is decimated? I guess, that this would solve the problem. Best regards, Kai

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Segfault error
by Jace Bradford King 19 Jun '14

19 Jun '14

Hello, I am running into a segfault error when trying to use tkmedit or tksufer. I am currently running OSX 10.7.5 and have the most current version of XQuartz installed. Below are the contents of the .xdebug files: .xdebug_tkmedit: tkmedit started: Wed Jun 18 10:58:41 2014 /Applications/freesurfer/tktools/tkmedit.bin bert brainmask.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/jaceking Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: .xdebug_tksurfer: Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut I also get a "Segmentation fault" note when trying to launch qdec. Do you have suggestions on how to fix this? Thanks in advance for your assistance. Best, Jace King

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