Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

mri_vol2surf
by Abdullah Ishaque 09 May '18

09 May '18

External Email - Use Caution Hi, It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps. I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses. Here's what I've done so far: 1. recon-all for all the subjects 2. Used bbregister to register the native T2 scans to the conformed T1 scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01) 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space) The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful! Let me know. Thanks!

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inherent smoothing
by Joost Janssen 09 May '18

09 May '18

External Email - Use Caution Dear Doug, I'd like to determine the inherent smoothing of ?h.thickness in my sample. What is the best way to do this? Thanks, -joost

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Errors are occurring after FreeSurfer Installation
by stdp82＠virgilio.it 09 May '18

09 May '18

External Email - Use Caution This errors are occurring when we test FreeSurfer Installation on our server: 1) ubuntu01:/usr/local/freesurfer/subjects> mri_convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... niiWrite(): error opening file sample-001.nii.gz ERROR: failure writing sample-001.nii.gz 2) ubuntu01:/usr/local/freesurfer/subjects> recon-all -i sample-001.nii.gz -s bert -all mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or directory. 3) ubuntu01:/usr/local/freesurfer/subjects> freeview -v sample-001.mgz freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory Thanks Stefano

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recon-all(about Installation' command) error
by subin oh 09 May '18

09 May '18

External Email - Use Caution Hello, Freesurfer Developer when I run the 'Test your FreeSurfer Installation' command (Example1~Example3) (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) I got the following errors pop up like this: Sorry for I'm a beginner.. Thanks very much for any suggestions! Best Regards, Subin Oh -------------------------[Example1~Example2]--------------------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/ FSFAST_HOME /Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer//subjects MNI_DIR /Applications/freesurfer//mni FSL_DIR /usr/local/fsl bash-3.2$ export c bash-3.2$ export SUBJECTS_DIR=/Application/freesurfer/subjects/subj01 bash-3.2$ cp $FREESURFER_HOME/subjects/sample-001.mgz usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directoy bash-3.2$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/chan/sample-001.mgz, -1): could not open file bash-3.2$ mri_convert sample-001.mgz fsample-001.nii.gz mri_convert sample-001.mgz fsample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/chan/sample-001.mgz, -1): could not open file bash-3.2$ mri_convert sample-001.mgz fsample-001.nii.gz mri_convert sample-001.mgz fsample-001.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... mghRead(/Users/chan/sample-001.mgz, -1): could not open file bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/subj01 bash-3.2$ recon-all -i sample-001.nii.gz -s subj01 -all ERROR: cannot find sample-001.nii.gz Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed May 9 12:43:41 KST 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting bash-3.2$ recon-all -i fsample-001.nii.gz -s subj01 -all ERROR: cannot find fsample-001.nii.gz Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed May 9 12:43:50 KST 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting----------------------… -------------------------------[Example3]------------------------ bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/ bash-3.2$ recon-all -s subj01 -all Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# MotionCor Wed May 9 12:56:55 KST 2018 ERROR: no run data found in /Applications/freesurfer/subjects/subj01/mri. Make sure to have a volume called 001.mgz in /Applications/freesurfer/subjects/subj01/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s subj01 exited with ERRORS at Wed May 9 12:56:55 KST 2018 For more details, see the log file /Applications/freesurfer/subjects/subj01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ----------------------------------------------------------------

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Problem with template longitudinal pipeline
by Laura van Velzen 09 May '18

09 May '18

External Email - Use Caution Dear FreeSurfer experts, We are trying to run FreeSurfer v5.3 on our longitudinal imaging data using the longitudinal pipeline. We first processed both time points cross-sectionally. The output of this step looks fine for both time points. We then performed step 2: creation of a template from both time points and step 3: longitudinally processing both time points. All steps run without errors, but the output of steps 2 and 3 look abnormal (please see images attached), so there appears to be something wrong in the creation of the template. We also have some subjects with data from only one timepoint and ran the longitudinal pipeline for these subjects as well (as was recommended on the wiki) and the output of steps 2 and 3 look fine for these subjects, so there appears to be an issue in creating the template based on both time points. The acquisition parameters at both time points are the same as far as we know. There is nine years between both measurements, and most of our subjects are between 50 and 60 years old at the second measurement. We have attached the recon.all.log file for one of our subjects. We hope you have some suggestions what the problem might be and how we could check this. Many thanks in advance for your help! Kind regards, Laura van Velzen & Julia Binnewies

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-cw256 flag in recon-all
by JAVIER ROJO MUÑOZ 08 May '18

08 May '18

External Email - Use Caution Hello FreeSufer developers, We're trying to have a small quality control pipeline when executing recon-all. As a part of this, one doubt came to us, and couldn't find an answer: Is the -cw256 flag applied always or only when the FOV is larger than expected? Also, when executing -autorecon1 and -autorecon2 separately, should we use this flag only in -autorecon1 or also in -autorecon2 and -autorecon3? I tried applying only to -autorecon1 and it worked apparently, but I don't know if I'm missing something. We're using the following version of Freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I would be more than grateful for any help, and sorry if that might be a lame question. Sincerely, Javier Rojo MuÃ±oz -- JAVIER ROJO MUÑOZ Universidad Politecnica de Madrid

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Re: [Freesurfer] problem using mri_vol2label for subcortical regions
by Lucia Billeci 08 May '18

08 May '18

External Email - Use Caution Dear Douglas, thanks a lot. This can solve my problem. Could you please give my some explanations about how to open and use the tool? Thanks Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci(a)ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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Re: [Freesurfer] transforming functional volumes to MNI without resampling
by David Beeler 08 May '18

08 May '18

External Email - Use Caution Alright thanks, mri_coreg looks a little better than bbregister. But similar to bbregister, using 6 dof results in a brain that is a little too small and using 12 dof has both scaling and translation issues. What would be the way to use CVS? I tried using the m3z from mri_cvs_register as described in my first message, but got those weird artifacts (http://web.mit.edu/dsbeeler/www/images/m3z-mni.png) DB ------------------------------------------------------------------------ Douglas N. Greve wrote: Use mri_coreg instead of bbregister. Make sure to use 12 DOF. You could use CVS as well since that is non-linear > ------------------------------------------------------------------------ On 05/07/2018 04:11 PM, David Beeler wrote: > > > Hi Doug, > Ok so if I am understanding correctly, SPM or FSL will be better at > registering functional data to CVS or MNI space for group analyses than > freesurfer will be because they have the capability of doing nonlinear > registrations. If that's the case I may give SPM a shot and compare the > results. > But if I were to use freesurfer to do this registration, is there something > better than the following commands?: > bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --bold > > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg > --no-resample --nearest > Adding --12 to bbregister and using the same mri_vol2vol as above actually > makes the transformation much worse, is there something I'm missing? I will > use SPM if I have to, but I feel like there is probably something smarter I > could be doing with freesurfer. And for clarification, is the --12 flag in > bbregister making the registration affine (ie accounting for translation, > rotation, scaling, and sheers)? > Thanks again for your help, much appreciated! > DB > ------------------------------------------------------------------------ > Douglas N. Greve wrote: > If that is really what you want to do, you should use a tool appropriate > for this type of analysis (eg, SPM and FSL have non-linear intersubject > registration) > ------------------------------------------------------------------------ > > On 05/04/2018 01:13 PM, David Beeler wrote: > > > > > > Hi Doug, > > > > funcVol is an individual functional resting state scan. We are doing > > some clustering analyses and trying to visually compare the clustering > > across subjects (I would be a bit sketched out trying to quantify the > > overlap between subjects due to individual differences in anatomy, > > etc, but just looking at it might give us a clue on what is going on). > > We do all our analyses in the individual subject's native space, but > > it's hard to see what the similarities / differences are. > > > > If not bbregister, what would be the correct way to align all subjects > > to a common space? > > > > Thanks, > > DB > > ------------------------------------------------------------------------ > > Douglas N. Greve wrote: > > What is funcVol? An individual functional? If so, then use --12 (12 dof > > to account for scaling). In general, we don't recommend doing cross > > subject registration with BBR as it is really not appropriate for that > > kind of thing. > > ------------------------------------------------------------------------ > > On 05/03/2018 01:30 PM, David Beeler wrote: > > > > Hi, > > > > I'm trying to register and transform some raw functional data > > (108x108x72x175, 2mm iso voxels) to MNI space, while keeping the low > > res dimensions. > > > > I have tried: > > bbregister --s MNI152_FS --mov funcVol --reg func2mni.lta --init-fsl > > --bold > > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg > > --no-resample --nearest > > mri_vol2vol --mov funcVol --reg func2mni.lta --o funcVolMNI --fstarg > > --no-resample > > > > And this looks pretty good, but not perfect... the functional data is > > oriented correctly but the brain seems to be a centimeter or two > > smaller in multiple dimensions, see: > > > > http://web.mit.edu/dsbeeler/www/images/bbregister-mni.png > > > > I'm not too surprised since the MNI brain is blurry and oddly round, > > but presumably there is a way to do this transformation more > > accurately. I've run mri_cvs_register for this subject using the --mni > > flag: > > > > mri_cvs_register --openmp 8 --mni --mov $subjID --outdir $mniDir > > > > And for other applications I use this m3z file to transform volumes > > between MNI orig.mgz and individual subject orig.mgz, but is there a > > way to use it to transform functional data to MNI space while keeping > > the functional dimensions? > > > > I could do: > > > > mri_vol2vol --mov funcVol --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz > > --reg register.dof6.lta --nearest --o template-in-anat.nii.gz > > > > mri_vol2vol --noDefM3zPath --targ $SUBJECTS_DIR/$subjID/mri/orig.mgz > > --mov template-in-anat.nii.gz --m3z > > $mniDir/final_CVSmorph_tocvs_avg35_inMNI152.m3z --o > > template-in-MNI-m3z.nii.gz --nearest > > > > But not only is this unideal because it requires upsampling the > > functional data to 256x256x256, it also gets these funky wavy distortions: > > > > http://web.mit.edu/dsbeeler/www/images/m3z-mni.png > > > > > > Any thoughts are appreciated, thanks! > > > > -DB > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Longitudinal hippocampal subfields analysis problem
by Tamir Eisenstein 08 May '18

08 May '18

External Email - Use Caution Hi FreeSurfer experts, I've tried running the longHippoSubfieldsT1.sh command on a subject with 2 time points on FS 6.0, and it seemed working well while running. However, after about 10 hours of processing it "ended" with the following message, and no files have been created in any of the subject's /mri folders: Applying LTAtransformInterp (resample_type 0) writing to discreteLabelsResampledT1_tp_1.mgz... numberOfLabels: 25 Rasterizing mesh...here: 25 /usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45: 103248 Killed "${exe_dir}"/SegmentSubfieldsT1Longitudinal $args @#@FSTIME 2018:05:05:21:24:27 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 e 36809.26 S 113.13 U 3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280 w 377770 I 48432510 O 1579840 L 5.28 3.10 2.20 @#@FSLOADPOST 2018:05:06:07:37:57 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49 With appreciation for your help, Best, Tamir

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Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields
by Iglesias Gonzalez, Eugenio 08 May '18

08 May '18

External Email - Use Caution Dear Mark, Just to make sure we’re on the same page: I’ll say that two images are in the same voxel space when they have the same size (in voxels, e.g., 256x256x256) and the same vox2ras matrix - the one that maps voxel coordinates to RAS (physical) coordinates. The subfield segmentation is indeed in the same RAS coordinates as your native T1, but not in the same voxel space. One option that you have is to convert your subfield mask to the voxel space of the T1, with the option –rl (“reslice like”) of mri_convert: For probabilistic masks: mri_convert subfield_prob.mgz subfield_prob_T1voxelSpace.mgz -rl norm.mgz -odt float For discrete masks or segmentations, you can use a similar command, but with nearest neighbor interpolation: mri_convert subfield_mask.mgz subfield_mask_T1voxelSpace.mgz -rl norm.mgz -odt float -rt nearest I hope this helps! Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mark Wagshul <Mark.Wagshul(a)einstein.yu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 2 May 2018 at 20:57 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields External Email - Use Caution Hi. I am just getting my feet wet with running my subjects through the Freesurfer processing stream, so the following question night be a bit trivial (I hope): I have run qvlSegmentHippocampal subfields on one of my subjects, and it completed just fine with what seem to be the appropriate outputs in the subject’s mri folder. I have another 100 subjects to run, but want to make sure I can accomplish what I would like to on this subject first. The images which I see are sub-images, i.e. these have fewer voxels compared to the original image, but in the native T1 space resolution (= 1 mm3). I would now like to register the subfields in the native space (my DTI/NODDI maps are already registered into this space), to obtain mean values within each subfield. How can I transform these sub-field images back into the native T1 space, or is there a method within Freesurfer to perform the math (e.g. similar to fslmaths)? Thanks, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [instein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Freesurfer May 2018