Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

Surface label to volume and then back to surface
by David Beeler 03 Apr '18

03 Apr '18

Hi all, Sorry in advance, this is a bit of an annoying one! I am trying to use freesurfer's automatically generated MT label as a parcel to constrain activity measured during a functional MT localizer. I am currently doing my analysis in the volume and I'd like to transform the MT surface label into the subject's volume functional space (i.e. the same space as the sig.nii.gz for a particular contrast), take the voxels in sig.nii.gz that are within the MT label, and project them back onto the surface (preferably to be viewed as an overlay with freeview). I will eventually run the analysis on the surface as well (making this much less roundabout, but I also use volume parcels so understanding how to correctly go between the volume and surface is important to me). In my pipeline I start off by running preproc-sess, then I register and transform my preprocessed functional data (fmcpr.nii.gz) to the subject's anatomical (without upsampling). After doing mkanalysis and mkcontrast, I run selxavg on this volume. So the functional data is aligned with the anatomical, but still has low res dimensions. If it's not too much to ask, would it be possible to provide the specific commands to do all these transformations properly? I'll provide some of the commands I've tried below so you can see where I'm going wrong: First I want to transform the MT label to the functional volume. I've tried: mri_label2vol --subject $SUBJID --label $SUBJECTS_DIR/$SUBJID/label/rh.MT.label --o $OUTPUTDIR/rh.MT.volume.anat.nii.gz --temp $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --identity --fill-ribbon --hemi rh ...which I would expect to put the label in high resolution anatomical volume space (orig.mgz), but it doesn't fill the graymatter ribbon nicely at all. I then use mri_vol2vol to transform to functional/sig.nii.gz space (I could also just downsample with mri_convert since I've already aligned my sig.nii.gz to my anatomical, this gives me the same result). I am using regheader here, is this okay? mri_vol2vol --regheader --mov $OUTPUTDIR.rh.MT.volume.anat.nii.gz --targ meanfunc.nii.gz --o rh.MT.volume.func.nii.gz --nearest ...and this works pretty well, but it's a little sparse so I may need to dilate it with mri_morphology. I think this step is fine. Next I use matlab to take the voxels in sig.nii.gz that are also in rh.MT.volume.func.nii.gz and I save that as a new volume, say constrainedsig.nii.gz. Now I want to transform constrainedsig.nii.gz to the surface. I have tried going directly using the register.dof6.lta generated from preproc-sess: mri_vol2surf --mov constrainedsig.nii.gz --reg register.dof6.lta --projfrac 0.5 --interp nearest --hemi rh --o $OUTPUTDIR/constrainedsig_surface.nii.gz ... and this is in the right area, but its shape doesn't match the shape of the original label. So I've also tried backtracking and doing another vol2vol and then vol2surf with regheader: mri_vol2vol --regheader --mov constrainedsig.nii.gz --targ $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --o $OUTPUTDIR/constainedsig_anatvolume.nii.gz mri_vol2surf --mov constrainedsig_anatvolume.nii.gz --hemi rh --regheader S02 --o $OUTPUTDIR/constrainedsig_anatsurface ...and while this ends up in the right place, it is really patchy (looking kind of like twisty zebra stripes). Seems to me like it has the wrong dimensions or something, but mri_info says it's the same dimensions as the volume I originally created with mri_label2vol. Any help is much appreciated, thanks! David

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Percent Signal Change
by Sarah Cole 03 Apr '18

03 Apr '18

Hi, Could someone please let me know how to get the percent signal change for raw signal intensity? I think the cespct.nii.gz gives me the contrast as %. However, I am not sure about dividing h.nii and h-offset.nii. What are they? Thank you

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Hemodynamic Lag Shift
by Sarah Cole 03 Apr '18

03 Apr '18

Hi Doug, I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks. We used to shift our raw data by 2 TRs when we were using SPM. How can we do this in FreeSurfer? Thank you, Sarah

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mirroring fsaverage labels between hemispheres
by Abigail Noyce 02 Apr '18

02 Apr '18

Hi, I have pored over (I think) all of the mailing list postings about cross-hemisphere mapping and I can't quite figure out how to do this. I have a bunch of labels on fsaverage, and I want to be able to check/visualize the relationship between lh and rh versions of the labels. I can do mri_label2label to map from fsaverage to fsaverage_sym, but that doesn't do the right thing, and fsaverage doesn't have the same kind of xhemi registration structure that "normal" subjects get with surfreg --xhemi. I guess I could back-project onto a normal subject and then project to fsaverage_sym, but that seems like an unnecessary step. How can I get mirror-projected labels from fsaverage on fsaverage_sym? Thanks! Abby -- Abigail L. Noyce, Ph.D. Psychological & Brain Sciences Boston University anoyce(a)bu.edu 617-440-3640

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mri_watershed Error: indices out of bounds
by Darko Komnenić 31 Mar '18

31 Mar '18

Dear experts, while running recon-all on FreeSurfer 5.1.0 I encountered the following error: mri_watershed Error: indices out of bounds I searched the email archive and found this thread: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… My problem seems identical to the one described by initial poster. The suggestion was to try the following command: set mdir=$SUBJECTS_DIR/$subject/mri mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz $mir/nu.mgz When I tried it, the message I got was: mri_add_xform_to_header: could not open source file /nu.mgz No such file or directory And indeed such file does not exist in the mri subfolder of my current subject's folder. Any further suggestions on how to fix this? Like the person asking originally, this is the only participant where it happened, for others, recon-all finished without error and all the images were acquired in the same scanner. Thanks in advance! Best, Darko

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Re: [Freesurfer] convert labels to volume in MNI?
by gj 30 Mar '18

30 Mar '18

Hi, I loaded the 2mm MNI152 template and the mri_label2vol outputs in mricron, and I saw that the labels are completely outside the template. So, I know now to use freeview rather than the deprecated tkmedit so I can also load the original atlas labels to check against (using the 2mm MNI152 template as background) -- in any case, I don't even see the labels, I guess because the ROIs/masks lie outside the display. I'm also not sure what the equivalent of tkmedit's overlay-reg is for freeview? I assume my not loading one is why I get the error, "Label coordinate out of bound" when I try and load the original atlas labels (in fsaverage space) on the MNI152 template? Thank you! Gina P.S. Can't find a straightforward way to reply with the entire thread when receiving only a digest from the listserv -- reply to the digest takes the freesurfer-request address rather than the list address and the button on the website for archives only gives the option of replying directly to the person who posted)...what am I missing? ------------------------------ Douglas Greve dgreve at mgh.harvard.edu Tue Mar 27 14:01:16 EDT 2018 how are you verifying that it is not in the right place? You should view it on the 2mm MNI152 using freeview. Also, your label should be a label in fsaverage space. On 3/27/18 9:52 AM, gj wrote: > Hi, > > Newbie question....I want to take FreeSurfer labels (from an atlas in > fsaverage space) and convert it into a volumetric NIFTI mask. I ran the > following command, but I must be missing something because the output is > not in the right space (far too posterior): > > $FREESURFER_HOME/bin/mri_label2vol \ > --label $ll \ > --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ > --reg $FREESURFER_HOME/average/mni152.register.dat \ > --fillthresh .5 \ > --o $wd/${ll}.nii > > Am I perhaps supposed to first create the volumetric file without > mapping into MNI space and then use tkregister2? > > Thanks in advance for any help or advice! > Gina

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error rerunning recon-all (exited with ERRORS)
by Anna Daniels 30 Mar '18

30 Mar '18

Dear FreeSurfer team, after editing the brainmask.mgz (manually or with gcut), brain.finalsurfs.manedit.mgz and/or adding control points, recon-all was rerun in a loop for several subjects with the respective options *-autorecon-pial* (1) or *-autorecon2 -autorecon3* (2), which resulted in the following error for only some of the subjects (while others worked fine): (1) #@# Mask BFS Mo 19. Mär 02:35:22 CET 2018 /scratch/annadan1111/MABT1T2/reruncrosstest_pial/23358_T1_fs_edit/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 mghRead(/scratch/annadan1111/MABT1T2/reruncrosstest_pial/23358_T1_fs_edit/mri/brainmask.mgz, -1): read error mri_mask.bin: could not read mask volume brainmask.mgz Linux node011 2.6.32-696.18.7.el6.x86_64 #1 SMP Wed Jan 3 19:31:16 CST 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 23358_T1_fs_edit exited with ERRORS at Mo 19. Mär 02:35:23 CET 2018 (2) 3d normalization pass 1 of 2 white matter peak found at 110 Cannot allocate memory Linux node098 2.6.32-696.20.1.el6.x86_64 #1 SMP Thu Jan 25 08:47:49 CST 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 44538_T1_fs_edit exited with ERRORS at Do 29. Mär 01:28:15 CEST 2018 Attached are the respective recon-all.log files in case they may be helpful. We also could not detect any similar post in the mailing list. FreeSurfer version 6.0.0 Thank you and Happy Easter greetings from Berlin, Anna

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Building from source -- autoconf error
by Alle Meije Wink 29 Mar '18

29 Mar '18

I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system. (64 bit, using g++ 4.9 for compilation) After $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev $ cd dev $ cvs update -d # just to make sure $ ./setup_configure I get these messages: rm -rf autom4te.cache libtoolize --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: linking file `config/ltmain.sh' libtoolize: putting macros in `m4'. libtoolize: linking file `m4/libtool.m4' libtoolize: linking file `m4/ltoptions.m4' libtoolize: linking file `m4/ltsugar.m4' libtoolize: linking file `m4/ltversion.m4' libtoolize: linking file `m4/lt~obsolete.m4' libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. aclocal aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist Which looks like a not-(anymore)supported use of autoconf? I found one previous message on the list about autotroll https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.… that provided another version of configure.in which might solve the issue. And it did in the original case but sadly not for me. I get the same error message also with the new configure.in -- there should probably be a configure.ac? If anyone knows how to make this work (e.g. by modifying the configure script) that would be fantastic.

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Re: [Freesurfer] defining input images in a for-loop in recon-all
by Darko Komnenić 29 Mar '18

29 Mar '18

Hi Bruce, thanks for the reply. I only have one acquisition per subject. I guess I can make a separate text file with a list of paths to dicoms and then somehow try to pair the path and the subject name in the recon-all command. > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] defining input images in a for-loop in > recon-all > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1803291007011.1834(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Darko > > sorry, you need to sort this out yourself as there is no way for us to > know where the dicoms are. An alternative is to create each subject dir, > create the 00?.mgz files (if you have more than one acquistion) in the > <subject>/mri/orig dir, then run recon-all without the -i flag. If you use > -i you need to figure out a way to find one slice in the correct dicom > series for each subject. > > cheers > Bruce > > > On > Thu, 29 Mar 2018, Darko Komneni? wrote: > >> Dear experts, >> I would like to run a for-loop in FreeSurfer 5.1. so that I can have >> multiple subjects analyzed over >> the holiday, without having to come to the lab and start each of them >> myself. I searched the >> previous emails in this list and know that I can make a file with a >> subject list, and then have the >> loop go through that file. >> I was wondering, however, how to handle the -i part of recon-all command? >> Each subject in a loop >> needs to have one brain image assigned - I don't think FreeSurfer will >> know where to look for images >> just by telling it what the subject name is. >> Thanks in advance for any help!

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A new member to freesurfer mailing list
by XIAO YANG 29 Mar '18

29 Mar '18

Hi FreeSurfer experts , I am Xiao Yang, who is a visiting research fellow in McLean Hospital, Harvard Medical School. I am writing to ask to be added to the FreeSurfer mailing list. Here is my email address: yangxiaokxmyt(a)gmail.com Thank you so much! Best wishes, Xiao Sent from Mail for Windows 10

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Freesurfer March 2018