Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

Combining multiple transforms into one register.dat file for oblique angle acquisitions
by Ajay Kurani 16 Oct '14

16 Oct '14

Dear Freesurfer users, I had a question regarding how to combine multiple register.dat files into one file. Essentially, I have a T1 image which I created masks for in native space. I then import the T1 image into freesurfer and run through the recon-all pipeline. Subsequently, I use bbregister in order to register my last EPI timepoint to the T1 image and generate the register.dat file and when viewing the files the overlap looked great. 1) mri_convert -i m${sub}.T1.nii --in_type nii -o ${sub}.T1.FS.mgz --out_type mgz 2) bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat --init-header --bold --frame $NP_last --nearest --template-out ${sub}.RS.template.nii 3) tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat --surf I wanted to take my brain (freesurfer) and masks(native space pre-freesurfer) and the aseg file and then register this to the EPI scan and used the following commands: 4) Convert mask to freesurfer format mri_convert -i ${loc_dir}/spm/c1${sub}.T1.nii --in_type nii -o ${out_dir}/__c1${sub}.T1.mgz --out_type mgz 5) Take mask to brain freesurfer formatted space mri_vol2vol --mov ${out_dir}/__c1${sub}.T1.mgz --targ $SUBJECTS_DIR/${sub}_FS/mri/brainmask.mgz --regheader --o ${out_dir}/__c1${sub}.T1.FS.mgz --no-save-reg --nearest 6) Apply the inverse transforms of EPI to Anatomical so that the anatomical scans and masks are now registered with the EPI scan in native space (pre-freesurfer file). mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/brain.mgz --o $out_dir/__brain_FS2spm.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ $SUBJECTS_DIR/${sub}_FS/mri/aseg.mgz --o $out_dir/__aseg_FS2spm.nii --inv --reg $out_dir/${sub}_RS_register.dat --interp nearest mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ ${out_dir}/__c1${sub}.T1.FS.mgz --o $out_dir/__c1${sub}.T1.FS2spm.nii --inv --no-save-reg --reg $out_dir/${sub}_RS_register.dat --interp nearest The steps above work great when the T1, generated masks and EPI were all acquired plumb (no oblique angle). I tried using the steps for when the T1 (10.144 deg from plumb) and EPI (12.44 deg from plumb) were taken at 2 different oblique angles and the images did not register correctly when going back to native space. I essentially would not be able to apply the inverse register.dat directly to the aseg and mask files because when I did they did not look oriented correctly in afni (I did also try 3dWarp -deoblique on the resulting freesurfer files but this did not work for the oblique images). I wanted to see if I created two registration.dat files (One for EPI to Freesurfer's brain.mgz and another for the masks to Freesurfers brain.mgz) and combine these transforms into one file which I can pass to the native space images via commands in 6) so that they transforms are correct. OR am I wrong and there is a simpler way to achieve this. Please specify the commands to use in either case. Thanks, Ajay

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Re: [Freesurfer] Freesurfer Digest, Vol 128, Issue 21
by Claire Morley 16 Oct '14

16 Oct '14

Hi Bruce, Thanks so much for your response. It`s just when I try to type the "test commands" from this link: https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. The Freeview command does work, but the commands for tkmedit, tksurfer, and qdec do not work. Therefore, my tksurfer command was simply: tksurfer bert rh pial. When I try this, the computer spits out nothing, no error, no window pops up, nada. I have made sure that the bert rh pial file does exist in the surfs and it does (I run this while in my freesurfer/subjects directory. The only thing I can think of is perhaps I installed something wrong, but I followed all of the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall. I wonder however, if in my SetUpFreeSurfer.sh file the script includes the tk tools. Since it`s a third party package, are they automatically installed? As I said before, I did this on another Mac at my other lab where Freesurfer had been previously installed and the command for tksurfer worked perfectly. So I dont think its my command but something with the configuration that`s going wrong. Could also be affecting qdec`s inability to run? Also I see here: https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferGeneralUsag… that there are two other ways to launch Tksurfer. However the one which suggests lauching it from Freesurfer with the surface button makes it sound like there is a Freesurfer GUI, however I have yet to discover one. Is there a way to launch this as well? I really appreciate all of your help! I know this will be a lot easier once I get everything up and running. All the best, Claire Here is my full script from my SetUpFreeSurfer.sh file: #!/bin/bash -p # # SetUpFreeSurfer.sh # # This is a sample SetUpFreeSurfer.sh file. # Edit as needed for your specific setup. # The defaults should work with most installations. # Set this to the location of the freesurfer installation. if [ -z $FREESURFER_HOME ]; then export FREESURFER_HOME=/usr/local/freesurfer/stable5-pub fi # Set this to your subjects/ dir, usually freesurfer/subjects/ if [ -z $SUBJECTS_DIR ]; then export SUBJECTS_DIR=$FREESURFER_HOME/subjects fi # Set this to your functional sessions dir, usually freesurfer/sessions/ if [ -z $FUNCTIONALS_DIR ]; then export FUNCTIONALS_DIR=$FREESURFER_HOME/sessions fi # Specify the location of the MINC tools. # Necessary only if the script $FREESURFER_HOME/FreeSurferEnv.csh # does not find the tools (and issues warnings pertaining to # the following two environment variables, which have example # locations that might need user-specific modification): #export MINC_BIN_DIR=/usr/pubsw/packages/mni/current/bin #export MINC_LIB_DIR=/usr/pubsw/packages/mni/current/lib # ... or just disable the MINC toolkit (although some Freesurfer # utilities will fail!) #export NO_MINC=1 # Enable or disable fsfast (enabled by default) #export NO_FSFAST=1 # Call configuration script: source $FREESURFER_HOME/FreeSurferEnv.sh On Wed, Oct 15, 2014 at 6:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Issues launching tksurfer (Bruce Fischl) > 2. Re: Issues launching tksurfer (dgw) > 3. Re: Transform labels in Diffusion space into MNI space > (Corinna Bauer) > 4. Re: mri_anatomical_stats for volume (Douglas Greve) > 5. Re: problem with gyrification index extraction (Douglas Greve) > 6. Re: problem with gyrification index extraction (elisa veronese) > 7. Re: Transform labels in Diffusion space into MNI space > (Douglas Greve) > 8. Re: Transform labels in Diffusion space into MNI space > (Corinna Bauer) > 9. Re: Transform labels in Diffusion space into MNI space > (Douglas Greve) > 10. Re: Transform labels in Diffusion space into MNI space > (Corinna Bauer) > 11. Re: Transform labels in Diffusion space into MNI space > (Corinna Bauer) > 12. Re: Transform labels in Diffusion space into MNI space > (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 15 Oct 2014 08:30:14 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Issues launching tksurfer > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1410150829570.23626(a)nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Claire > > can you send us the full output of the command from the time you type > tksurfer > > thanks > Bruce > On Wed, 15 Oct 2014, Claire Morley wrote: > > > Good Morning, > > I have a quick question regarding the launch of tksurfer. I have recently > > downloaded Freesurfer onto a Mac OSX after having some experience with > it on > > a previous Mac. However, it had been preinstalled on that Mac, and I am > > afraid that I have perhaps installed it wrong on this one as when I test > the > > launching of qdec and tksurfer, nothing happens. The terminal doesn`t > spit > > out a command error, but it never launches the program. This was also a > > problem on the previous Mac for qdec but not for tksurfer. Therefore, I > have > > tried to install everything again from square one and am not sure why now > > neither program is launching. I am simply trying to test the command > > "tksurfer bert lh pial". My environment is setup with Freesurfer and I am > > trying to launch from the surfs directory, as that worked on the previous > > Mac, but it is still giving me nothing. Any tips you could provide me > with? > > > > All the best, > > Claire > > > > > > -- > > > > We shall not cease from exploration. And the end of all our exploring > will > > be to arrive where we started and know the place for the first time- T.S. > > Eliot > > > > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 15 Oct 2014 09:00:37 -0400 > From: dgw <dgwakeman(a)gmail.com> > Subject: Re: [Freesurfer] Issues launching tksurfer > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CADM2BTh_RpZUHEOBJgWFDmQta-= > qA2nmj+jkiBMrv5Zu38sFsw(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Claire, > > How did you install FreeSurfer? Did you follow the instructions here: > http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall > > ? > HTH, > D > > On Wed, Oct 15, 2014 at 4:02 AM, Claire Morley > <clairemorley2014(a)u.northwestern.edu> wrote: > > Good Morning, > > I have a quick question regarding the launch of tksurfer. I have recently > > downloaded Freesurfer onto a Mac OSX after having some experience with > it on > > a previous Mac. However, it had been preinstalled on that Mac, and I am > > afraid that I have perhaps installed it wrong on this one as when I test > the > > launching of qdec and tksurfer, nothing happens. The terminal doesn`t > spit > > out a command error, but it never launches the program. This was also a > > problem on the previous Mac for qdec but not for tksurfer. Therefore, I > have > > tried to install everything again from square one and am not sure why now > > neither program is launching. I am simply trying to test the command > > "tksurfer bert lh pial". My environment is setup with Freesurfer and I am > > trying to launch from the surfs directory, as that worked on the previous > > Mac, but it is still giving me nothing. Any tips you could provide me > with? > > > > All the best, > > Claire > > > > > > -- > > > > We shall not cease from exploration. And the end of all our exploring > will > > be to arrive where we started and know the place for the first time- T.S. > > Eliot > > > > > > > > _______________________________________________ > > 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. > > > > > ------------------------------ > > Message: 3 > Date: Wed, 15 Oct 2014 10:19:01 -0400 > From: Corinna Bauer <corinnab83(a)gmail.com> > Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI > space > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > CAJOsP4K_5Vr15qWzj6tN3AUrYVsbuO9j7bYOu4eszBjw3rtweg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Doug, > > I'm not sure why, but the registration is off. In tkregister2, the > "coronal" appears as an axial slice and vice versa, while the sagittal is > rotated 90 degrees compared to the target. I did the following: > 1. mni152reg --s MAE_06072013 > 2. tkregister2 --mov > > /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz > --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg > > /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg > 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz > --reg MAE_06072013/register.dat --surf > > Up until this point, everything looks good and well registered. > > 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim > MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat > > > Corinna > > On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu > > > wrote: > > > > > Hi Corinna, once you do #1, you can concatenate the register.dat with the > > mni152.2mm.reg.dat like this > > > > mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat > > > > Check > > tkregister2 --mov dti.nii --targ > > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat > > > > mri_vol2vol --mov dti.nii --targ > > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o > > dti.in.mni.nii > > > > doug > > > > > > > > On 10/14/14 2:57 PM, Corinna Bauer wrote: > > > > Hello all, > > I am wanting to put labels currently in diffusion space into MNI space. > > Does this make sense or is there a more straight forward way? > > > > 1. mni152reg the subject's structural into MNI space > > 2. inverse transform the MNI in the the subject's T1 space > > 3. Use bbregister to align the DTI to the T1 space > > 4. inverse transform the MNI into DTI space using mri_vol2vol using the > > registration from step 3? > > > > Cheers, > > > > Corinna > > > > > > _______________________________________________ > > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps:// > 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 > > > > > > 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. > > > > >

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a problem
by Ting Li 16 Oct '14

16 Oct '14

Hi, experts, I am trying to use the template fsaverage_sym and tried to map the same set of vertices onto the left and right pial surface. Surprisingly, these vertices on the two surfaces did not correspond to the same anatomical cortical regions. Sometimes, they correspond to each other very badly. For instance, one is mapped onto the lateral surface on the left pial surface, the other may be mapped onto the medial surface on the opposite hemisphere, I can not see their symmetry. Any comment? How can I establish the correspondence between the rh and lh pial surfaces? Ting

2 1

Registering a parcellation from MNI_2mm space to subject native spac
by Marcelo Mattar 15 Oct '14

15 Oct '14

Hello, I'm new to Freesurfer, and I'm lost in something that I believe is very basic. I have a parcellation of the brain in .nii format that is currently in MNI space (2mm). I would like to move this parcellation to subject native space, so that I can extract the BOLD timeseries from each region of the parcellation. I understand that an option I have is to simply use FSL tools such as FLIRT or FNIRT and move the parcellation file to subject space (using nearest neighbor interpolation). However, given that I have reconstructed the subject's anatomy to the surface space, I believe I can do a better job that just an affine transformation. What should I do in this case? 1) Is there any freesurfer tool that would allow me to register a volume to another volume, but aided by surface information? 2) If so, what steps should I follow to extract BOLD timeseries for each subject from the parcellation regions? Thank you very much, -- Marcelo Mattar University of Pennsylvania

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Fwd: recon-all error
by Kate Riggall 15 Oct '14

15 Oct '14

Hello, I am using freesurfer for the first time, and I am having issues when I try to run recon-all for my first subject. My details are: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: jessie/sid Kernel info: Linux 3.13.0-37-generic i686 Subject name: Y03 Command line: fsuser@xubuntu-VirtualBox:~/host/Sprachlernen$ recon-all -all -subjid Y03 Error message: "recon-all exited with ERRORS at Fri Oct 10 02:42:23 EDT 2014 " recon-all.log: attached. I am running freesurfer within Virtual Box on a windows host, and my subjects folder is in a shared folder /home/fsuser/host and is called /home/fsuser/host/Sprachlernen/Subjects I first mounted this shared folder by entering sudo mount -t vboxsf Kate /home/fsuser/host and then designated this as my subjects folder by entering export SUBJECTS_DIR=/home/fsuser/host/Sprachlernen/Subjects I then created the subject data directory using recon-all -i Y03_1 -i Y03_2 -subjid Y03 before running recon-all -all. Any assistance would be much appreciated. Kind regards, Kate Riggall

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ROI analysis problem...
by Joseph Andreano 15 Oct '14

15 Oct '14

Hi Freesurfer community, I'm having a difficulty extracting signal from an ROI using funcroi-config and funcroi-table-sess. Every time I try to run the commands, I get the same error message: "ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created." Now, so far as I can tell, neither of these reasons for the error apply in my case. My approach has been to generate labels from the annotation in each subject's aparc.a2009s+aseg using mri_cor2label: mri_cor2label --c $s/mri/aparc.a200s+aseg.mgz --id 11149 --l $s/label/l_circ_inf_insula.label Then I applied the ROI commands below: funcroi-config -label l_circ_inf_insula.label -analysis NMASA_block_induction.lh -roi l_circ_inf_insula.roicfg funcroi-table-sess -roi l_circ_inf_insula.roicfg -analysis NMASA_block_induction.lh -contrast negVneut -sf induction_all.lst -o l_circ_insula_inf.dat ... and this leads to the error message above. The thing is, as the label is being generated from the subject's own segmentation, they're not coming from different subjects or hemispheres, and I see no reason to think that the surface has changed. Does anyone see the problem here? I'm working off of some pretty old code, so it may be that the commands I'm using are out of date. So if there's a better way to generate labels from the aparc-aseg and extract signal, please let me know. Thanks, Joe _________________________________ Joseph M. Andreano, PhD Research Fellow Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

1 0

Transform labels in Diffusion space into MNI space
by Corinna Bauer 15 Oct '14

15 Oct '14

Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way? 1. mni152reg the subject's structural into MNI space 2. inverse transform the MNI in the the subject's T1 space 3. Use bbregister to align the DTI to the T1 space 4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3? Cheers, Corinna

3 9

Trying to make GCA atlas, problem with talairach file
by N/A N/A 15 Oct '14

15 Oct '14

Hi Freesurfers, I am trying to make an atlas using the GCA algorithm and the error message I just got is asking for the talairach.xfm file. The scans I am using were originally run through freesurfer 3.1 and talairach processing was not done. What do you suggest I do to use these scans in my atlas I am trying to create? Kind regards, Alexarae

1 0

mri_anatomical_stats for volume
by Vy Dinh 15 Oct '14

15 Oct '14

Dear experts, Can one use mri_anatomical_stats to extract volume information? I have a set of labels that has been mapped to each subject's native space (using mri_label2label; the original labels were extracted from group comparisons using mri_glmfit). I have successfully extracted the thickness measures using mri_anatomical_stats and am curious if this can be done with the labels from my volume group comparisons as well. This is the command I used for the extracting the thickness measures: mris_anatomical_stats -l $label -t $hemi.thickness -b -f $sublabel $sub $hemi Thanks in advance, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

2 3

Issues launching tksurfer
by Claire Morley 15 Oct '14

15 Oct '14

Good Morning, I have a quick question regarding the launch of tksurfer. I have recently downloaded Freesurfer onto a Mac OSX after having some experience with it on a previous Mac. However, it had been preinstalled on that Mac, and I am afraid that I have perhaps installed it wrong on this one as when I test the launching of qdec and tksurfer, nothing happens. The terminal doesn`t spit out a command error, but it never launches the program. This was also a problem on the previous Mac for qdec but not for tksurfer. Therefore, I have tried to install everything again from square one and am not sure why now neither program is launching. I am simply trying to test the command "tksurfer bert lh pial". My environment is setup with Freesurfer and I am trying to launch from the surfs directory, as that worked on the previous Mac, but it is still giving me nothing. Any tips you could provide me with? All the best, Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

3 2

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Freesurfer October 2014