Re: [Freesurfer] .lta vs .dat questions

External Email - Use Caution Also - what does the "fscale" in the .lta file refer to? On Wed, Oct 18, 2023 at 1:40 PM Corinna Bauer wrote: > Thanks, Yujing. > > Do you know why the output of mri_vol2vol would be different if using the > .lta vs the .dat

Re: [Freesurfer] .lta vs .dat questions

.@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer > *Sent:* Wednesday, October 18, 2023 1:07 PM > *To:* Mailing Freesurfer List > *Subject:* [Freesurfer] .lta vs .dat questions > > > > *External Email - Use Caution

[Freesurfer] .lta vs .dat questions

External Email - Use Caution Hi all, Can someone please explain the difference between .lta and .dat and why the registration looks different using the two file types? If bbregister outputs were already checked and edited (if needed) using the .dat file, is there a way to convert

[Freesurfer] Postdoctoral fellow in multimodal neuroimaging

. • Experience with multimodal neuroimaging datasets is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, and their C.V. to Corinna Bauer (corinna_ba...@meei.harvard.edu). Additional details can be found at: https://secure

Re: [Freesurfer] matlab runtime error

freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Corinna Bauer < > corinna...@gmail.com> > *Date: *Wednesday, September 1, 2021 at 4:58 PM > *To: *Mailing Freesurfer List > *Subject: *[Freesurfer] matlab runtime error > > *External Email - Use Caution

[Freesurfer] matlab runtime error

External Email - Use Caution Hi all, I ran a few subjects successfully through7.1.1, but when I got to check the surfs in freeview I get an error about the Matlab runtime libraries below. However, I already have those libraries and the 2014b runtime environment installed on my Ubu

[Freesurfer] Diffusion MRI postdoc position

send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( corinna_ba...@meei.harvard.edu). Additional details can be found at: https://secure-web.cisco.com/1PRcDuRd4mfRf2yIwKkDZ9B

Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data

External Email - Use Caution Hi Bruce, I am just following up on this. Were you able to get mri_normalize to run on this mp2rage data? Thanks, Corinna On Wed, May 5, 2021 at 6:50 PM Corinna Bauer wrote: > Great, thanks. The nu.mgz is attached. > > Corinna > >

[Freesurfer] postdoc opportunity in relaxometry and diffusion MRI

career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( corinna_ba...@meei.harvard.edu). Additional details can be found at: https://secure-web.cisco.com

[Freesurfer] Postdoctoral fellowship opportunity in diffusion MRI and functional vision

in Boston, MA We are seeking a full-time postdoctoral fellow to work with Dr. Corinna Bauer on an NIH-funded project investigating the impact of neonatal thalamic injury on the development of vision-processing networks in the brain and corresponding visuo-perceptual dysfunctions. The project

Re: [Freesurfer] Discrepancy in volume calculated for thalamic nuclei in FreeSurfer

del is a > tetrehdra mesh, and that is used to compute partial volume. > doug > > > > On 6/29/2020 6:06 PM, Corinna Bauer wrote: > > External Email - Use Caution > Hello all, > > We are working on calculating the volume of thalamic nuclei in our > part

[Freesurfer] Discrepancy in volume calculated for thalamic nuclei in FreeSurfer

External Email - Use Caution Hello all, We are working on calculating the volume of thalamic nuclei in our participants and noticed that there is often a discrepancy in measured volume in the ThalamicNuclei.v12.T1.volumes.txt and the volume calculated for the same thalamic nucleus

Re: [Freesurfer] MNI coordinates from Thalamic nuclei

wrote: > External Email - Use Caution > > Why not represent thalamic nuclei as the actual masks? Thalamic nuclei > are not single points. > > > > Matt. > > > > *From: * on behalf of Corinna > Bauer > *Reply-To: *Freesurfer support list > *Date

[Freesurfer] MNI coordinates from Thalamic nuclei

External Email - Use Caution Hi all, Is there a way to obtain the MNI coordinates for the thalamic nuclei? Thanks Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] Project functional region into white matter

voxels that were in WM. but the 1st is definitely cleaner > > On 12/18/19 2:52 PM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Ok thanks! The first option sounds like it might provide a cleaner > > result, since the second would dila

Re: [Freesurfer] Project functional region into white matter

o > roidilated-in-wm.mgz > > > On 12/18/19 2:33 PM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Hi Doug, > > Yes, I have GM ROIs in CVS space and I'd like to create a > > corresponding WM ROI for each of them that ex

Re: [Freesurfer] Project functional region into white matter

Do you want > to do something like a wmparc.mgz? > doug > > On 12/18/19 9:55 AM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Hello all, > > > > I have a series of functionally-defined ROI volumes (.nii format) th

[Freesurfer] Project functional region into white matter

External Email - Use Caution Hello all, I have a series of functionally-defined ROI volumes (.nii format) that I'd like to project into the white matter to then be used for tractography. So far the vols have been brought from cvs_avg35 space into subject space from using mri_vol2

[Freesurfer] thalamus_proper or whole_thalamus volume measurement?

External Email - Use Caution Dear all, For the new thalamus nuclei segmentation there is a measurement for the whole left and right thalami. The values are different from the thalamus_proper values. Which output should be reported as the volume for the whole thalamus? Thank you

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Great, thank you! Best, Corinna On Thu, Jun 29, 2017 at 12:09 AM, Thomas Yeo wrote: > Hi Corinna, > > You can download here: https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_ > JNeurophysiol11_SplitLabels.zip?dl=0 > > Regards, > Thomas > > > On Thu, Jun 29,

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Dear Dr. Yeo, Our research group is currently trying to segment the Yeo atlas into separate labels, but just came across this thread which indicates that you have already done this. Would you be willing to re-share the link to your previously extracted individual labels from your 7 and 17 networks

Re: [Freesurfer] mri_cvs_register failure from missing shared lib

> > On 04/25/2017 01:49 PM, Corinna Bauer wrote: > > Hi Zeke, > > > > I am also having this same problem. Even after completing the steps you > > listed above. I am running Ubuntu 12.04. > > > > Any suggetions? > > > > Thanks > > &

Re: [Freesurfer] mri_cvs_register failure from missing shared lib

Hi Zeke, I am also having this same problem. Even after completing the steps you listed above. I am running Ubuntu 12.04. Any suggetions? Thanks On Wed, May 28, 2014 at 1:50 PM, Z K wrote: > You will need to install libboost v1.41 onto your system. You should be > able to install it using yum

Re: [Freesurfer] volume in native space of .vtk file in mni152 space

Hi Antonin, Thank you for your input. I will give mri_cvs_register a try. Best, Corinna On Mon, Apr 24, 2017 at 10:24 AM, Antonin Skoch wrote: > Dear Corinna, > > I am not sure what is (or whether is) something wrong with your commands, > but in any case I would be cautious of interpretation

[Freesurfer] volume in native space of .vtk file in mni152 space

Dear all, I have a series of .vtk files in MNI152 1mm space from an external thalamus atlas outlining specific thalamic nuclei. I would like to put these into native subject space and calculate the volume from each nuclei. I would imagine that I would do the following: 1. run mni152reg --s --1 o

Re: [Freesurfer] seed to seed resting state?

command in Freesurfer v5.3.? Is it command in v6.0? > > Thanks and best, > > Jinsong > > > > > On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Try fcseedcor. Run with -help to get docs >> >> >> O

Re: [Freesurfer] seed to seed resting state?

Hi, just following up on this question to see if there were any suggestions for how to best complete seed to seed RS analysis in FreeSurfer. Thanks! Corinna On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer wrote: > Hi all, > > I was just wondering if it was possible to do seed to see

[Freesurfer] seed to seed resting state?

Hi all, I was just wondering if it was possible to do seed to seed resting state analysis in freesurfer, rather than seed to voxel? I am wanting to examine connectivity within specific Yeo networks, using a spherical ROI as a seed. The spherical ROI will be generated from one of the peak areas of

Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster

Should be, so long as it is the uncorrected value. Is that the CWPmax? On Mon, Oct 3, 2016 at 2:57 PM, Douglas N Greve wrote: > In the table produced by glmfit-sim, the maximum vertex-wise uncorrected > -log10(p) is given. Is that enough? > > > On 10/03/2016 02:55 PM, Cori

Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster

d I use? Thanks Corinna On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer wrote: > Hello all, > > I would like to get a table of the uncorrected p-values to compare with > the corrected ones obtained using mri_glmfit-sim. I tried the following, > which outputs a table of clusters

[Freesurfer] Output uncorrected p-values using mri_surfcluster

Hello all, I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-

Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

t. > > > On 08/29/2016 02:53 PM, Corinna Bauer wrote: > > Sorry for not specifying. Yes, we are looking at difference in volume > > between the two groups using DODS. What is the most statistically > > sound... raw values, demeaning across the entire sample, or demeaning

Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

different between the two groups for ICV. On Mon, Aug 29, 2016 at 2:48 PM, Douglas N Greve wrote: > not sure what you are testing, but if you are, eg, looking at the > difference between two groups regressing out ICV, then it can make a > huge difference > > > On 08/29/2016 12:36

[Freesurfer] Results different between mean-centered and raw covariates -- glm_fit

Hello all, I am wondering why results would change completely for between group volume analysis when using demeaned/mean-centered ICV compared to using ICV as a covariate in mri_glmfit? See the figures below. Does demeaning the covariate inherently change the results comapred to the raw covariate

Re: [Freesurfer] errors in wm and pial boundaries

Hello, Have you been able to look at the data I sent over yet? It would be great to get a sense of what we can or cannot do to correct the boundaries. Thanks Corinna On Wed, May 25, 2016 at 12:05 PM, Corinna Bauer wrote: > Hi Bruce, just checking in to see if you have had an opportunity

Re: [Freesurfer] errors in wm and pial boundaries

Hi Bruce, just checking in to see if you have had an opportunity to take a look at the data I sent over? Thanks Corinna On Wed, May 18, 2016 at 6:19 PM, Corinna Bauer wrote: > Sure. I'm uploading now. The above is approximately slice 75, although the > control points/wm surface

Re: [Freesurfer] errors in wm and pial boundaries

m a single slice. If you upload the > subject and tell us the specific coordinates that you see problems in we > will take a look > > cheers > Bruce > On Tue, 17 May 2016, Corinna Bauer wrote: > > Hello all,We are analyzing data from our collaborators and are running into &g

[Freesurfer] errors in wm and pial boundaries

Hello all, We are analyzing data from our collaborators and are running into some difficulties with the accuracy of the pial and wm boundaries. The wm.mgz appears to follow the actual WM, independent of the wm surface boundary. Attached is an example showing two types of problems. 1. the WM surface

Re: [Freesurfer] mris_make_surfaces dimensions error

mand line? Sounds like you are using a > surface overlay as the cover_seg parameter instead of a volume one. Try > running mri_info on it to make sure it is a volume (i.e. 256x256x256). If > not, you will need to sample it into the volume with mri_surf2vol > > thanks > Bruce > > O

[Freesurfer] mris_make_surfaces dimensions error

Hello all, I am attempting to reshape the pial surfaces to fill the new boundaries in my edited ribbon.mgz file. I am using mris_make_surfaces with the -cover_seg flag but keep getting this error: ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2 height=1. Any suggestions?

Re: [Freesurfer] pial edits in subject with severe atrophy

Hi Bruce, I exported the ribbon.mgz to itksnap and was able to edit the grey matter to include the atrophic frontal areas. I am wondering if there is a way to have these edits reflected in the pial surface? Thanks. Corinna On Wed, Feb 10, 2016 at 4:02 PM, Corinna Bauer wrote: > ok tha

Re: [Freesurfer] pial edits in subject with severe atrophy

ok thanks. On Wed, Feb 10, 2016 at 3:40 PM, Bruce Fischl wrote: > not to my knowledge, but others may have developed something > Bruce > On Wed, 10 Feb > 2016, Corinna Bauer wrote: > > > Thanks, Bruce. > > In an earlier thread from '09 with a similar problem( &g

Re: [Freesurfer] pial edits in subject with severe atrophy

I should mention that the aseg file captures the GM outside the pial surface. On Wed, Feb 10, 2016 at 1:23 PM, Corinna Bauer wrote: > Thanks, Bruce. > In an earlier thread from '09 with a similar problem ( > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.h

Re: [Freesurfer] pial edits in subject with severe atrophy

an do if there is that big a lesion. If the > topology is wrong and you can't see tissue in those regions it's going to > be very hard > Bruce > > > On Wed, 10 Feb 2016, > Corinna Bauer wrote: > > > Dear Experts, > > > > I have a subject with severe

[Freesurfer] pial edits in subject with severe atrophy

Dear Experts, I have a subject with severe atrophy in bilateral frontal and parietal regions and after many rounds of edits to the brainmask, wm.mgz, and control points, these regions are still left uncaptured. Is there a way to edit the pial surface to include these grey matter regions? I am hesi

[Freesurfer] segmentation errors in subject with severe atrophy

Dear all, We are working on editing the segmentation of a subject with severe atrophy due to a seizure event that occurred during infancy. In portions of the parietal and frontal lobe the atrophy is so severe that freesurfer can't find any WM or GM. Is there a way to manually fill in the GM so that

[Freesurfer] aparc labels to grey white ratio

Hi all, What command would I use to apply the aparc labels to a different surface (e.g. to $h.ratio.mgh)?? The ratio file was created as follows: mri_vol2surf --src ${nu_mgz} --projfrac +0.35 --surf white --hemi lh --out ${subj_dir}/mri/lh.white.projfrac.pos35.mgh --regheader ${subject} --nor

Re: [Freesurfer] mri_glmfit-sim mc-z comapred to mc-full

e same as computing the glm. It has been a > while, but I remember the mc-z as being more conservative, but it is much > much faster. > > doug > > > On 2/3/15 10:12 AM, Corinna Bauer wrote: > > Hi all, > I am wondering what the specific reasons might be for choosing to ru

[Freesurfer] mri_glmfit-sim mc-z comapred to mc-full

Hi all, I am wondering what the specific reasons might be for choosing to run the mc-z simulation compared to mc-full? What are the pros and cons for each method for looking at group morphometry differences? Thanks Corinna ___ Freesurfer mailing list Fr

Re: [Freesurfer] strange artefact in T1 - stripe pattern

e > On Thu, 23 > Oct 2014, Corinna Bauer wrote: > > > Hello, > > I am analysing some structural data for collaborators and one of the > > datasets has a strange artefact in it. Is there any way to adjust for the > > intensity band

Re: [Freesurfer] Transform labels in Diffusion space into MNI space

MAE_06072013/register.dat -iim > MAE_06072013/mri/mni152.orig.mgz.reg -om MAE_06072013/newmnireg.dat > > doug > > > On 10/15/2014 10:33 AM, Corinna Bauer wrote: > > I tried your suggestion first and the registration was off, whereby > > the axial and coronal were sw

Re: [Freesurfer] Transform labels in Diffusion space into MNI space

gt; and see if it works. > doug > > > > On 10/15/14 10:29 AM, Corinna Bauer wrote: > > Doug, instead of using the register.dat (which was generated from > bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg > register.dat), I had to use the registration f

Re: [Freesurfer] Transform labels in Diffusion space into MNI space

> On 10/15/14 10:19 AM, Corinna Bauer wrote: > > 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 follow

Re: [Freesurfer] Transform labels in Diffusion space into MNI space

} --targ ${subj_dir}/mri/orig.mgz --reg register.dat --inv --o ${mri_indtispace}. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat Corinna On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer wrote: > Hi Doug, > >

Re: [Freesurfer] Transform labels in Diffusion space into MNI space

.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 d

[Freesurfer] Transform labels in Diffusion space into MNI space

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

Re: [Freesurfer] mris_divide_parcellation for white matter

${subj_dir}/smaller_labels mri_extract_label ${subj_dir}/mri/wmdivided.nii 3001 ${subj_dir}/smaller_labels/wm-lh-bankssts.nii On Mon, Jul 7, 2014 at 1:05 PM, Corinna Bauer wrote: > great, thanks! I'll give that a try and let you know how it goes. > > > On Mon, Jul 7, 2014 at 12:50 PM

Re: [Freesurfer] mris_divide_parcellation for white matter

gt; to the indices and change the name to be wm- instead of ctx- and include > those in the new ctab > > clunky, but it should work > > doug > > > On 07/07/2014 12:29 PM, Corinna Bauer wrote: > > the new white matter divided labels. I was not able to extract the > >

Re: [Freesurfer] mris_divide_parcellation for white matter

, Douglas N Greve wrote: > The name of which label? > > On 07/02/2014 02:00 PM, Corinna Bauer wrote: > > Whereby the label name is derived from which, the GM labels? i.e. > > lh.rostralmiddlefrontal_div3 > > > > > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fisch

Re: [Freesurfer] mris_divide_parcellation for white matter

I figured it out. Thanks for your help! On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer wrote: > Whereby the label name is derived from which, the GM labels? i.e. > lh.rostralmiddlefrontal_div3 > > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl > wrote: > >> y

Re: [Freesurfer] mris_divide_parcellation for white matter

Whereby the label name is derived from which, the GM labels? i.e. lh.rostralmiddlefrontal_div3 On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl wrote: > yes, or mri_binarize --match > > > cheers > Bruce > > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > And th

Re: [Freesurfer] mris_divide_parcellation for white matter

gt; cheers > Bruce > > > On Wed, 2 Jul 2014, Corinna Bauer wrote: > > Hi Bruce, >> >> I am trying to do just that using the following command line: >> mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown >> --volmask >> --o ${subj_dir}/m

Re: [Freesurfer] mris_divide_parcellation for white matter

recrate the wmparc from it, which might do what > you want. > > cheers > Bruce > > > On Tue, 1 Jul 2014, Corinna > Bauer wrote: > > > hello, > > I was wondering if it was possible to use mris_divide_parcellation on > wh

[Freesurfer] mris_divide_parcellation for white matter

hello, I was wondering if it was possible to use mris_divide_parcellation on white matter labels. Thanks, Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information i

Re: [Freesurfer] longitudinal recon-all -long error

> > /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz > > in freeview to see if maybe the file is corrupted. > > Best, Martin > > > > On 04/25/2014 03:46 PM, Corinna Bauer wrote: > > Hello, > I am on the recon-all -long step of th

[Freesurfer] longitudinal recon-all -long error

Hello, I am on the recon-all -long step of the longitudinal processing stream and the final time point exits with errors at the mri_convert stage. mri_convert -at /home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta -odt u

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

in the folder just above the mri folder? > > On 04/10/2014 11:20 AM, Corinna Bauer wrote: > > Hi Doug, > > Following the example in recon-all.log, I tried this: mri_aparc2aseg > > --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o > > mri/wmdivided

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

at 11:11 AM, Douglas N Greve wrote: > Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log > file for an example command line that generates wmparc.mgz > > doug > > On 04/10/2014 09:52 AM, Corinna Bauer wrote: > > For creating corresponding wm segmentat

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

, 2014 at 10:28 AM, Corinna Bauer wrote: > Perfect. Thanks! > > > On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> >> you'll need to figure it out from the volume itself by loading the seg >> with both -seg and -

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

ou what the id is > > doug > > On 04/09/2014 09:41 AM, Corinna Bauer wrote: > > In the mri_extract_label, there is a label number. Where would I find > > this for the new labels? > > > > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035 > > ${subj_di

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

Should I make up my own LUT for the new ROIs that specifies some colour and label number? On Wed, Apr 9, 2014 at 10:00 AM, Corinna Bauer wrote: > It looks like the FreeSurferColorLUT.txt does not contain the label number > for the newly created labels (divided from the desikan atlas). &g

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

It looks like the FreeSurferColorLUT.txt does not contain the label number for the newly created labels (divided from the desikan atlas). On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl wrote: > $FREESURFER_HOME/FreeSurferColorLUT.txt > > cheers > Bruce > On Wed, 9 Apr 2014, Corinn

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

8/14 6:00 PM, Corinna Bauer wrote: > > Hi Doug, > After I have the labels then in each subject's T1 space, I will need to > then put them into diffusion and resting state space. > > I already have scripts that put the parcellations into subject-specific > diffusion

Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

annot, see example 6) > > doug > > On 04/08/2014 04:54 PM, Corinna Bauer wrote: > > Hello all, > > > > I am planning to use mris_divide_parcellation to split the Desikan > > atlas into smaller ROIs, but will need the new ROIs to be consistent > > between subj

[Freesurfer] mris_divide_parcellation same divisions between subjects

Hello all, I am planning to use mris_divide_parcellation to split the Desikan atlas into smaller ROIs, but will need the new ROIs to be consistent between subjects. Can I achieve this if I register each subject to fsaverage space and then apply the inverse transform to the divided parcellations (

[Freesurfer] Discrepancy between volume generated by aparcstats2table and mri_segstats

Hello all, I have noticed a discrepancy in the volumes generated by aparcstats2table and mri_segstats using aparc+aseg. Which is correct? I am using version 5.3. Thanks, Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

[Freesurfer] Talairach failure in 5.3 but not in 5.2

Hello all, I have 2 subjects that failed autorecon-all at the same Talairach step. Both subjects successfully completed autorecon-all in version 5.2. Here is the output from one of the subjects. Any suggestions? Corinna # #@# Talairach Fri Feb 28 12:39

Re: [Freesurfer] expand GM label into white matter

Hi Doug, I don't see anywhere a seg.mgz. mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17 Corinna On Tue, Nov 5, 2013 at 11:38 AM, Corinna Bauer wrote: > I think that the first option you provided is more along the lines of what > I'm looking for. Th

Re: [Freesurfer] expand GM label into white matter

wmparc.mgz so you don't overwrite what is > there. When it is done, there will be a WM label for each cortical label. > Is this what you want? It won't do this for subcortical structures. > doug > > > On 11/04/2013 12:25 PM, Corinna Bauer wrote: > >> ok thanks, I

Re: [Freesurfer] expand GM label into white matter

--o mask17.dil2.wm.mgz # seg 17 > inside WM > mri_concat mask17.mgz mask17.dil2.wm.mgz --sum --o mask17+wm.mgz # seg > 17 plus dilation into WM > > doug > > > On 11/04/2013 11:38 AM, Corinna Bauer wrote: > > Hello all, > > Is there a way to exp

[Freesurfer] expand GM label into white matter

Hello all, Is there a way to expand a GM label into the white matter by n voxels? Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended

[Freesurfer] aparcstats2table error

Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas thickness --tablefile symm_aparc_stats_rh.txt error: ERROR: The stats file /media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.s

Re: [Freesurfer] Fornix labelled as corpus callosum in patient with periventricular leukomalacia

Hi Bruce, I was just wondering if you had any suggestions on how to fix the corpus callosum labels? Corinna On Wed, Aug 14, 2013 at 11:49 AM, Corinna Bauer wrote: > In general, it mostly looks ok. There are regions which are labelled as > hypointensities, but should be CSF or gray

Re: [Freesurfer] epi correction of fmri data

and phase > > doug > > > > > > On 05/03/2013 01:05 PM, Corinna Bauer wrote: > >> Should the phase image be in rads? and does the magnitude image need to >> be skull-stripped first? >> >> >> On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer >

Re: [Freesurfer] epi correction of fmri data

Should the phase image be in rads? and does the magnitude image need to be skull-stripped first? On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer wrote: > thanks Doug, I will give that a try. > > > On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu&g

Re: [Freesurfer] epi correction of fmri data

E_DIFF --esp YOUR_ESP \ > --vsm bold/b0dcmap.nii.gz > > When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the > command lines. > > doug > > > On 05/03/2013 12:16 PM, Corinna Bauer wrote: > >> Yes, I am using FSFAST. >> >> >

[Freesurfer] epi correction of fmri data

Is there a way to correct fmri data for epi distortions in freesurfer? Or does the data need to be first fun through FSL's B0 unwarping? Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/

Re: [Freesurfer] mkbrainmask error with libmeshclass.so

actually, on closer look, adding those lines to the FSL config did not fix the problem. However, if I call bet2 by typing fsl5.0-bet2, then it works. I am not sure why, but to call anything from fsl I have to first put fsl5.0- first. On Tue, Apr 16, 2013 at 2:40 PM, Corinna Bauer wrote

Re: [Freesurfer] mkbrainmask error with libmeshclass.so

On Tue, Apr 16, 2013 at 12:07 PM, Douglas Greve wrote: > Hi Corinna, I hate to pass the buck, but I think you'll have to contact > the FSL people to get it sorted out. > doug > > > > On 4/16/13 9:31 AM, Corinna Bauer wrote: > > Yes, if I just type bet2 I still get

Re: [Freesurfer] mkbrainmask error with libmeshclass.so

2/2013 03:56 PM, Corinna Bauer wrote: > > Hello all, when running preproc-sess, I got this error message: > > ERROR: could not determine file for > > > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain > > Try running mkbrainmask-sess with -per-run

[Freesurfer] mkbrainmask error with libmeshclass.so

Hello all, when running preproc-sess, I got this error message: ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain Try running mkbrainmask-sess with -per-run I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . -fsd bold

Re: [Freesurfer] bbregister error with hardi data

gt; Re-run bbregister and let me know if this works. > > doug > > > > On 03/25/2013 01:11 PM, Corinna Bauer wrote: > >> yes, this file exists. >> >> >> On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr

Re: [Freesurfer] bbregister error with hardi data

yes, this file exists. On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve wrote: > Can you verify that > /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**brainmask.mgz > exists? > doug > > > On 03/25/2013 12:55 PM, Corinna Bauer wrote: > >> sure. Here is the d

[Freesurfer] bbregister error with hardi data

Hello all, I am attempting to run bbregister on 4D HARDI data that has already been motion, eddy, and epi-distortion corrected in fsl. I run the command: bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat and get a number of errors that seem to beg

[Freesurfer] error in longitudinal template creation

Hi all, I was creating the longitudinal template for a subject when I got this error while on the third time point. Is this a memory problem or is it something else? Thanks, Corinna Resolution: 0 Iteration(single-prec): 1 -- diff. to prev. transform: 0.0425184 Iteration(single-prec): 2mri_

Re: [Freesurfer] Problem creating longitudinal template file

ay 14, 2012 at 10:29 PM, Martin Reuter wrote: > Hi corinna, > Can you send the corresponding call to recon-all that your script > generates? > > Best Martin > > On May 14, 2012, at 18:27, Corinna Bauer wrote: > > Hello all, > I am trying to create a template for longi

[Freesurfer] Problem creating longitudinal template file

Hello all, I am trying to create a template for longitudinal processing and am running into some problems generating the file. I have many subjects so I am running a batch script. I am using version 5.1.0 Any suggestions? Thanks! Corinna Here is my script: #!/bin/tcsh setenv FREESURFER_HOME /App

Re: [Freesurfer] fscalc size mismatch error

Would the best solution be to average the frames of the first file or can I specify just one frame? Corinna On Mon, Jul 11, 2011 at 1:17 PM, Corinna Bauer wrote: > Looks like it is because one of the files has multiple frames. > > mri_info first file: > > Volume information for

Re: [Freesurfer] fscalc size mismatch error

your second. > > Can you run the command and copy-paste the output into an email? Also, run > 'mris_calc' with '--verbosity 10'. That will print out additional (useful) > information. > > > > On 7/11/11 12:25 , Corinna Bauer wrote: > >> When runni

[Freesurfer] fscalc size mismatch error

When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Co

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