[Freesurfer] Gyrification Index

External Email - Use Caution Dear FreeSurfer experts, I try to explore the Gyrification Index of both hemispheres in a population. For this I computed the LGI using the Freesurfer pipeline and used the command suggested in previous mails: mri_segstats --slabel subject lh $SUBJE

[Freesurfer] surface based analysis using Infant FS

External Email - Use Caution Dear FS experts, We are currently exploring the Infant Freesurfer pipeline for surface based analysis in our cohort. The generated surfaces seem reasonable, but now we are wondering, how to proceed. To our understanding, by looking at the recon-all

[Freesurfer] mri_vol2vol

//dmri/xfms/anatorig2diff.bbr.dat --o /mri/dtifit_MD_registered.nii.gz Thanks a lot Celine ___ 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] Tracula - set echo spacing

Hi Anastasia and Tracula experts, We are running a new set of tracula analysis from Bay 6 and are wondering how do we define the number of echo spacing in the dmrirc file. Is it a number that we get from the header of the field map dicoms? set echospacing = ... Thanks a lot Celine -- Celine

Re: [Freesurfer] mri_cvs_register using high resolution images

the recon directory, they are aligned althouth they don't have the same format (I am always confused about that...) Celine > > Oh, I see you do not have a recon for your high res volume. Could you try > the below mri_vol2vol command with an additional -lta flag that has the > t

Re: [Freesurfer] mri_cvs_register using high resolution images

Thank you Lilla for the suggestion. You mean that I should run mri_cvs_register on the high res volume, is that correct? In that case, how can I specify the input volume? I did not find in the --help a way to specify manually the file to be registered, just the subject id. Thank you again Celine

[Freesurfer] mri_cvs_register using high resolution images

g freeview, they are not registered (while the output of mri_cvs_register for that subject was perfectly registered to the template). Would you have an advice to help me on that? Many thanks Celine ___ Freesurfer mailing list Freesurfer@n

[Freesurfer] TRACULA: distance between tract sections in pathstats.byvoxel.txt

between 2 sections along one tract? Thank you Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list

Re: [Freesurfer] Problem with a recon edit

sulci were already with a value of 0 in the WM.mgz, it can be helpful to change it to 1. Thanks a lot for the tips (and also the visualization tip, super helpful :-) Celine > Hi Celine, > > I took a look at you data, and made some edits to the wm that help to push > out the surfaces to

Re: [Freesurfer] Problem with a recon edit

Hi everyone I don't know if someone had the chance to look at the data we uploaded for advice to edit the recons (see below). Thank you so much Celine On Fri, 2015-01-16 at 11:43 -0500, Celine Louapre wrote: > Thanks Bruce > The aseg is correct, no ventricule labeled there (I was u

Re: [Freesurfer] Problem with a recon edit

n the left hemisphere was already present after autorecon2. I have uploaded the recon directory there: https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/32464/1/2115a25100be43906c26359fbbd1ed08 Thank you again :-) Celine On Fri, 2015-01-16 at 11:03 -0500, Bruce Fischl wrote: > H

[Freesurfer] Problem with a recon edit

ime I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radi

Re: [Freesurfer] Scatter plot from mri_glmfit analyses

way to work around, or should I just try to do it only from non pvr glm analyses? Celine > > X and C have different numbers of columns. What was your mri_glmfit > command line? If you used a --pvr, then the pcc script will not work. > doug > > On 09/22/2014 01:21 PM, Ce

Re: [Freesurfer] Scatter plot from mri_glmfit analyses

fast_glm_pcc (line 28) Xc = X*C'; And also I found this info in the script WARNING: X must have a column of 1s or both X and y must have been demeaned before the glm. But I am not sure about what it means. Attached are Xg.dat and C.dat files. Thanks again for your help Celine > >

Re: [Freesurfer] Scatter plot from mri_glmfit analyses

Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat? The cache.th13.abs.sig.ocn.annot contains the significant clusters it that correct? So to get individual mean values from cluster 1 for example where should I look? Thanks! Celine > > Have you run mri_glmfit-sim? It will

[Freesurfer] Scatter plot from mri_glmfit analyses

Celine On 05/31/2012 06:09 AM, Knut J Bjuland wrote: > Hi > > I am trying to calculate correlation coefficient using freesurfer GLM > for associations between volumes and IQ. I found this ealier answar, > but the matlab script but the link appear to be dead. > > http:/

Re: [Freesurfer] select_talairach_point function?

Hi I just find out how to launch the command, it is in the terminal where tksurfer is running, after the % sign. (I didn't understand what the tcl window was meaning) Best Celine > Hi > I am sorry if my question is really basic, but I am choosing the seeds for > fsfast resting stat

[Freesurfer] select_talairach_point function?

vertex number on fsaverage surface, so that I can build the corresponding label that I could use for the fcseed-sess command. I found this previous email, and there seem to be a command to do that but I don't know how to launch this command select_talairach_point Thank you very much C

[Freesurfer] Extract seed from resting state networks mask (Yeo and Buckner maps)

Best Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

oh yes I see, I have renamed the dpath/${TRACT[$num_tract]} directories to have a backup, so the name is not correct anymore. Actually I didn't need to do that, I can just set a different name for the outputs pathpathstats.byvoxel.txt and pathstats.overall.txt Thanks Celine > > Hi Ce

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

TS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: fio_pushd: ${PATH_3T}${SUBJECTS_3T[$subj]}/dpath/fmajor_PP_avg33_mni_bbr ERROR: must specify at least one type of output Would you have some idea about that? Thank you very much Celine > > Hi Celine - That's an interesting question.

Re: [Freesurfer] Pb with a registration of diffusion images processed with tracula and anat images

from whom the 2 spaces are really different, it is easier to figure out about registration). So anatorig2diff means diffusion space to anat space? Thanks a lot Celine > > I concur. If this is the lowb.nii.gz from trac-all and brainmask.mgz from > recon-all, they will be in their respecti

[Freesurfer] Pb with a registration of diffusion images processed with tracula and anat images

e DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Departme

Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]

't it? > > > > doug > > > > > > On 2/17/14 10:41 PM, Celine Louapre wrote: >> The lesion_vol2vol volume is still not correctly overlapping the DTI. >> >> The only command that didn't give me registration issue is mri_convert >> wh

Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]

olate and then binarize the mask was one possible option). I can show you the results tomorrow if you prefer Celine > > what does it look like if you run > > tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1 > > > > On 2/17/14 10:00 PM, Celine Louapre wrote

Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]

freeview maybe? or actually all the volumes are already on the recons space so maybe I should not use any registration matrix? Celine > > oops, sorry! That command looks like it is correct. Can you say more > about what is going wrong? How are you determining that something is > going w

[Freesurfer] Resample a mask on diffusion images using bbregister registration matrix

threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot Best Celine -- Celine Louapre, MD-PhD Research

Re: [Freesurfer] resample lesion mask on diffusion images processed with tracula

lesion_WM_vol2vol.nii.gz in freeview, the voxel sieze is the same as the DTI images, but the lesions are not at the same place. That is why I thought I had picked the wrong registration file...? Celine > > Hi Celine - If the lesion mask is already in the space of the freesurfer > recon, you ca

[Freesurfer] resample lesion mask on diffusion images processed with tracula

t the registration file to use. And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension than the diffusion space? Thanks a lot in advance for your help Best Celine ___ Freesurfer mailing list Frees

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

in the formula, I would not be able to calculate the motion factor for this parameter because median, upper and lower quartile are all 0, is that correct (it would make (x-0/0-0))? Thanks for your help Celine > Hi Anastasia and freesurfer experts, > I am trying to get DTI values along the tra

[Freesurfer] Compute DTI metrics in NAWM in Tracula

exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at

Re: [Freesurfer] GLM p value display

Oh so we don't report the significance itself? because for example if we have a small cluster but highly significant, does the cluster-wise correction p value take it into account? (compared to a large cluster but with lower significance). I may not have completely got this. Thanks Doug C

[Freesurfer] GLM p value display

? Thanks for advices Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] glm_fit --prune

Celine > Yes thanks so much, it worked very fine > Celine > >> >> In that case, I think you will want to change the design at each voxel >> based on which subjects are present. I have not tried to do this with >> pvr, but there is no reason it should not work. To d

Re: [Freesurfer] glm_fit --prune

Yes thanks so much, it worked very fine Celine > > In that case, I think you will want to change the design at each voxel > based on which subjects are present. I have not tried to do this with > pvr, but there is no reason it should not work. To do this, create a > binary volume

[Freesurfer] glm_fit --prune

--pune flag, but I am not sure if it is the one to use. Thanks Celine ___ 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 only for the person to

[Freesurfer] glm_fit --pvr

depth? And the 2nd question would be: is the contrast correct to test the correlation between the 2 surfaces at each vertex? Thanks a lot for your help Celine PS: here is the terminal output: gdfReadHeader: reading ms_age_gender.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be d

[Freesurfer] visualizing a surface below the WM surface

couldn't find how to do it but maybe I didn't choose the correct keywords in the archives! Thanks so much for you help! Céline -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown,

Re: [Freesurfer] Using glmfit with 2 different sequences

Thank you. For the contrast, if I don't enter any other regressor, then it will be 1 -1? Celine > Hi Celine, use mri_glmfit with the --pvr option (pvr = per-vertex > regressor) > doug > > > On 10/30/2013 10:20 AM, cel...@nmr.mgh.harvard.edu wrote: >> Hi freesurfer tea

[Freesurfer] Using glmfit with 2 different sequences

region level? From what I understood, when we use glmfit, the regressors that we can put are single values like age, group, cognitive testing etc, but maybe not an entire surface? Thanks a lot Best, Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of

[Freesurfer] Tracula threshold path

obtain an ROI that is consistent among subjects or is is possible that I would get a very thin CST in some subjects, or a very wide cst for example? Thanks for your help Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room

Re: [Freesurfer] medial wall crossing surface

Hi Bruce The aseg is correctly labeled as regards right and left GM cortex, but definitely some voxels are belonging to both hemisphere. The filled.mgz is fine too. Should we delete from aseg the voxels that are at the border between the lh and rh? Thanks Celine > Hi Celine > > is

Re: [Freesurfer] medial wall crossing surface

ggest? > Thanks > Celine > > -- > Celine Louapre, MD > Research Fellow at Massachusetts General Hospital > Department of Radiology, MGH > > Building 149, Room 2301 > 13th Street > Charlestown, MA 02129 > ___ > Freesurfer

[Freesurfer] medial wall crossing surface

Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine

Re: [Freesurfer] DTI metrics along the whole tract?

aking a weighted metrics would be possible in order to remove values that are a bit far from the highest probability of the tract. Thanks a lot! Celine > > Hi Celine - Since 5.2, there are 2 types of measures in the > pathstats.byvoxel.txt file: The value at every point along the trajector

[Freesurfer] weighted DTI metrics for each section

your help. Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Unable to run trac-all on a subject from whom...

Hi again I am sorry I found out that I needed to delete this file IsRunning.trac and then it works again. Sorry for the inconvenience Best Celine > Hi Freesurfer team > I am very new with tracula so my problem might be very obvious. > > I previously run trac-all -prep on a patient a

[Freesurfer] DTI metrics along the whole tract?

file, but for the whole width of the tract? If not, do you see a way to sample the value of the diffusion metrics on a certain tract starting from the cortex (like with projfrac or projdist with the WM surface)? Thanks very much for your help Celine -- Celine Louapre, MD Research Fellow at