Re: [Freesurfer] Labelling SurfStat p-value surface map

External Email - Use Caution Hi Bruce, Thanks for your tip. Unfortunately, I am still running through an error... I have a matrix of 18715 elements regarding both hemispheres. The size of fsaverage5 is 20484 I believe, so I filled the remaining elements with zeros, and also tried

Re: [Freesurfer] Labelling SurfStat p-value surface map

External Email - Use Caution Me again, Also, here is how I save the matrix on matlab: M = nan(4,4); save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/lh_emb_' char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M); Thanks, Sincerely, Loïc Le ven. 21

Re: [Freesurfer] Problem with installation test

if you have multiple cores you can use -openmp which gives a pretty good speed increase up to about N=4 or 5 cheers Bruce On Thu, 20 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution Thank You. It's working now. But I can see the execution time is really slow.

Re: [Freesurfer] Registration of image volumes

what kinds of volumes are they and why are you registering them? cheers Bruce On Thu, 20 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution Hi freesurfer, I want to do registration on two image volumes nifti file. What are the commands I have to use to do the regis

Re: [Freesurfer] Labelling SurfStat p-value surface map

why do you have 18715 elements? How did you create it? You can run mri_info on the .mgz volume to see if it has the correct dimensions. BTW: you might repost your original question early next week if you haven't resolve things. Doug is back and probably has an easy way to do what you want ch

Re: [Freesurfer] Labelling SurfStat p-value surface map

I don't think it matters but I would use eye instead of nan for M. But the critical issue is where you get your data and what dimensions it has cheers Bruce On Fri, 21 Jun 2019, Loïc Daumail wrote: External Email - Use Caution Me again, Also, here is how I save the matrix on

Re: [Freesurfer] voxel coordinates of corpus collosum

can you send us the full command line and screen output? Doug might have an easy way to do it, but personally I would do it in matlab cheers Bruce On Fri, 21 Jun 2019, Sadia Sheikh wrote: External Email - Use Caution Thanks for your reply. I want to get the voxel coordinates

Re: [Freesurfer] Registration of image volumes

Hi Shrabani I'm not even sure what these are images of. If you are looking for general-purpose registration tools you can try ANTS or something like that. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution The fixed volume is my model v

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution These are skull images of axial representation. Can't I use freesurfer? Because here interpolation is important. On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl wrote: > Hi Shrabani > > I'm not even sure what these are images of. If you are looking for

Re: [Freesurfer] Registration of image volumes

not unless you also have an image of the whole brain. Even then I'm not sure it will do what you want, although I'm still not clear on exactly what you are doing. Registering one image of the skull to a model? Why? On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use Cau

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution So, you mean to say that two volumes need to be exactly same kind and having same information? So I have generated a skull foramina model(which is triangular mesh) from the fixed image volume. Now I want to register the model with a general patient data

[Freesurfer] WARNING: no voxels in AR1 computation

External Email - Use Caution Dear FreeSurfer experts, I am trying to run *mri_glmfit *on a series of concatenated volumes. mri_glmfit --y $SUBJECTS_DIR/concat/new_glm_input.mgh --fsgd Qdec/qdec.fsgd --mask fsaverage/label_volume/mask.mgz --glmdir glm_output --C $SUBJECTS_DIR/qdec

Re: [Freesurfer] Registration of image volumes

Hi Shrabani no, that's not really what I'm saying. In any case, I'm not sure FreeSurfer is the right tool for you to use for this. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution So, you mean to say that two volumes need to be exactly

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution So in which case, freesurfer is applicable. Because I got a suggestion for CT to CT registration, I can use freesurfer. Thanks On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl wrote: > Hi Shrabani > > no, that's not really what I'm saying. In any case,

Re: [Freesurfer] Registration of image volumes

Hi Shrabani you can read about FS on our wiki. We generally require a T1-weighted MRI as input and build models of lots of things from it (including skull, which will be more accurate if you also have a PD or T2-weighted image). cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote:  

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution Okay Thank You for your all the responses. On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl wrote: > Hi Shrabani > > you can read about FS on our wiki. We generally require a T1-weighted MRI > as input and build models of lots of things from it (includi

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution I am using elastix. And I think it does something similar like ANTS. Do you think I should get the proper output using elastix? On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh wrote: > Okay Thank You for your all the responses. > > On Fri, Jun 21, 201

Re: [Freesurfer] Registration of image volumes

Hi Shrabani I really don't know - I don't have any experience registering skulls. sorry Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution I am using elastix. And I think it does something similar like ANTS. Do you think I should get the proper

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution Okay, thank you. On Fri, Jun 21, 2019 at 2:24 PM Bruce Fischl wrote: > Hi Shrabani > > I really don't know - I don't have any experience registering skulls. > sorry > Bruce > > On > Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > > > > External E

[Freesurfer] I have a question for "Segmentation of thalamic nuclei."

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version.I filled out “segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR]”.In two computer, there were massages “segmentThamicNuclei.sh: Command not found”

Re: [Freesurfer] I have a question for "Segmentation of thalamic nuclei."

External Email - Use Caution Dear Gwang-Won, What version are you using? What’s the output of “recon-all –version”? Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Gwang-Won Kim

Re: [Freesurfer] translations and rotations from an affine transform matrix

If it is an LTA (not .dat file), you can use mri_coreg --mat2par ltafile There will be 9 values that come out: 1-3: translation in mm 4-6: rotation in deg 7-9: should all be 1s in this case On 6/20/2019 2:52 AM, Pfannmoeller, Joerg Peter wrote: Hello, is there a tool to extract the translations a

Re: [Freesurfer] Fwd: freesurfer picture

You will have to find the qdec output folder. There will be a subfolder for each contrast. Load the sig.mgh file in the contrast subfolder, eg, tksurferfv fsaverage lh inflated -aparc -overalay sig.mgh tksurferfv is just a convenient front end for freeview (fv) On 6/17/2019 1:56 PM, Abby tang wr

Re: [Freesurfer] Tksurfer and qdec: error sourcing and floating exception

tksurfer has some instabilities in it. It is obsolete and no longer being supported. Have you tried freeview? You can use tksurferfv which runs freeview with tksurfer options. On 6/12/2019 6:54 PM, Wafaa Sweidan wrote: External Email - Use Caution Hello all, I have been using freesurf

Re: [Freesurfer] bbregister- switched coronal and axial views error

What version of FS are you using? If before 6.0 (eg, 5,3), then it may be an error with the initialization. This is much improved in version 6. On 6/18/2019 5:38 PM, Wenzhen Zhao wrote: > External Email - Use Caution > > Dear list, > > After running preproc-sess on fmri data, bbr-sum was

Re: [Freesurfer] Within-subject vertexwise correlation

I'm not sure that this is a question we can answer. If you do smooth, then you should smooth both modalities the same amount. On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote: External Email - Use Caution Dear FS experts, I would like to compute within-subject correlation between two mo

Re: [Freesurfer] eTIV and brainmask mismatch on Philips data

If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping? On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote: External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We

Re: [Freesurfer] registration with bbr and determination of motion regressors with mcdat2mcextreg

That is fine. I don't think that there are any conventions you need to follow (it should just be an Nx6 matrix On 6/13/2019 8:45 PM, Pfannmoeller, Joerg Peter wrote: Hello, I have used bbr to register all EPI volumes in my time series to the brains of my participants. The fMRI time series at ea

Re: [Freesurfer] hippocampal subfield as CONN seeds

There are several things that will need to be done, and they can be quite tricky. Since you already have a registration between the fMRI and the MNI, you will have to create a rigid registration from the FS anatomical to the fMRI, then concatenate the registrations into a single registration. Yo

Re: [Freesurfer] examining between group differences using DODS

On 6/7/2019 2:29 AM, Avi Gharehgazlou wrote: External Email - Use Caution Hi experts, I want to examine between-group differences in LGI controlling for age, sex and surface area (all except sex demeaned). To do so, I ran the DODS model on QDEC selecting: - “diagnosis” and “s

Re: [Freesurfer] Confirmation regarding running GLM on command line stream

Hi, sorry for the delay. On 6/7/2019 3:33 AM, Avi Gharehgazlou wrote: External Email - Use Caution Hi experts, Will you please confirm below command lines I run to examine between group differences in LGI? I have 3 questions listed. I can’t run the below line, it gives an error: mris_p

Re: [Freesurfer] translations and rotations from an affine transform matrix

you can also use lta_convert to convert a .dat file to an LTA On 6/22/2019 2:12 AM, Greve, Douglas N.,Ph.D. wrote: If it is an LTA (not .dat file), you can use mri_coreg --mat2par ltafile There will be 9 values that come out: 1-3: translation in mm 4-6: rotation in deg 7-9: should all be 1s in thi

Re: [Freesurfer] 4dfp data format

I don't know. I'm cc'ing Avi. On 6/8/2019 1:04 AM, Francesca Pentimalli wrote: External Email - Use Caution Dear freesurfer experts, I am trying to use the 4dfp data format, but I am not able to find the 4dfp suite of tools developed by Dr. Avi Snyder. Can someone please point me in th

Re: [Freesurfer] Within-subject vertexwise correlation

External Email - Use Caution I effectively smoothed both modalities the same amount. The question is whether I should or not smooth before calculating within-subject correlation? Best, Matthieu Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écr

Re: [Freesurfer] Advantage of having skull for longitudinal processing?

Hi Adam, the longitudinal registration should not care, but the regular stream would like to have the skull in the image. This will help for a couple steps (full head talairach registration -> eTIV etc). Best, Martin > On 5. Jun 2019, at 03:57, Adam Martersteck wrote: > > External

Re: [Freesurfer] Applying Pial edits to Longitudinal

Hi Sierra, the long command should be recon-all -long C002d C002.base -mprage ….. same way as you called it the first time when using the -all flag. Best, Martin > On 8. Jun 2019, at 20:28, Sierra Ann Jarvis wrote: > > External Email - Use Caution > > > Hello Freesurfers