[Freesurfer] R: Re: R: import FS-FAST results in FSL

Yes I would like to open with fslview (FSL) the sig.nii.gz of each subject which is computed by seed-based analysis by FS-FAST. I have mask the sig.nii.gz by fslmaths -div I have run: mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg subj/rest/001/register.dof6.dat --hemi rh --o

[Freesurfer] 3dClustSim and Gaussian filter width

Dear Freesurfers, I am trying to use 3dclustsim in AFNI to determine the minimum number of voxel in a cluster to reach significance, my understanding is that in the command line the -fwhm s flag refers to the gaussian filter width and NOT the Gaussian Kernel, can anyone point me to how I might be

Re: [Freesurfer] R: Re: R: import FS-FAST results in FSL

Hi Stefano mri_vol2surf samples the volume onto the surface and saves it as a 1D list of values, one per surface vertex. You can't view that in fslview AFAIK - you need to load a surface in freeview/tksurfer and visualize it as an overlay on the surface. cheers Bruce On Tue, 27 Oct 2015,

Re: [Freesurfer] remove label from aseg

The indices should be different. Eg, 17 is left hippo, 53 is right hippo. If you click on them in freeview and different labels appear, then FS knows they are different On 10/24/15 9:29 PM, Jacobs H (NP) wrote: > Hi. > > Just one another related question: now that I was able to combine left and >

Re: [Freesurfer] Funcroi-Table-Sess Error

I think the problem is probably that you created the label from a volume whereas funcroi expects the label to come from a surface. Instead of using mri_cor2label and -label for funcroi-config, try using something like funcroi-config -annot aparc.a2009s G_and_S_cingul-Ant -analysis

Re: [Freesurfer] comparison of 4 groups: mri_glmfit or Qdec?

yes, use mri_glmfit doug On 10/26/15 3:34 AM, Sandy Schramm wrote: > Dear Experts, > > we want to compare data (thickness) of 4 groups (3 morbid groups and 1 > controll group). Both, Qdec and mri_glmfit, will do the same analyses. > But we are not sure, if the usage of Qdec is statistically

Re: [Freesurfer] remove label from aseg

Hi Doug, Yes, for the aseg they are. But not for the hippocampal subfields: left and right have the same color coding. I am creating one segmentation, including left and right hippocampal subfields and aparc, for partial volume correction. Any idea how I can make the labels for the hippocampal

Re: [Freesurfer] Centrum Semiovale Labels in Freesurfer

We changed the name to "unsegmented white matter" because we don't know whether they really represent centrum semiovale. We don't have an ROI that has been verified to be CS. doug On 10/25/15 7:10 PM, Syeda Maryam wrote: Hello Freesurfer experts, I needed to extract the centrum semiovale

[Freesurfer] hippocampal subfield viewing

Hello, I used recon-all -hippo subfields on an earlier version of free surfer (recon v 5.0, hippo v5.0 or 5.1). There is no documentation on your website on how to view the subfields in freeview with versions earlier than 5.2. I noticed when I load all the subfields into free view and use the

Re: [Freesurfer] QDEC output after Monte Carlo simulation

It may cover both, but the peak can only be in one, and it is the peak that is reported. On 10/25/15 9:55 AM, Annemarie Brandhofe wrote: Dear freesurfer experts, I have analyzed inter-group differences in cortical thickness using freesurfer 5.3.0 and QDEC. I have found one significiant

Re: [Freesurfer] remove label from aseg

The color is not important. The question is whether they have a different index. Can you confirm that lh and rh have the same index? On 10/27/15 11:53 AM, Jacobs H (NP) wrote: > Hi Doug, > > Yes, for the aseg they are. But not for the hippocampal subfields: left > and right have the same color

Re: [Freesurfer] hippocampal subfield viewing

Hi Danielle, from the mri directory of a subject, run freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and be a bit patient; it takes a

Re: [Freesurfer] remove label from aseg

I just checked again in freeview and indeed they have the same index (e.g. CA1 has value 206 for left and also for right). On 10/27/15, 5:01 PM, "Douglas Greve" wrote: >The color is not important. The question is whether they have a >different index. Can you confirm

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Thank you for your input. I noticed that if I follow literally all the steps in the wiki, my data which is ordered by variable 'family' (instead of subjects, in my case is number of members belonging to e.g. family_1) is shuffled. This happens after I run the command sortData below.

[Freesurfer] T1-coregistered fmri - output to .nii

Hi Freesurfers, I am interested in running a functional connectivity analysis outside of the Freesurfer environment, using freesurfer-derived ROIs I've run recon-all, and I have run preproc-sess to carry out initial fmri preprocessing steps (motion correction, warping to the anatomical, etc)

Re: [Freesurfer] Funcroi-Table-Sess Error

On 10/27/15 1:09 PM, Morenikeji Adebayo wrote: Hi Doug, Thanks for the help! So, you’re saying that: 1. By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using mri_cor2label, I’ve created volume labels Correct 1. The commands ‘funcroi-config' and 'funcroi-table-sess'

[Freesurfer] Minc-tools - cannot find required library hdf5 - Ubuntu 12.04

Hi everybody. Could anyone help me please? I've downloaded minc-tools source code to compile and install on Ubuntu 12.04, but I've got an error when try to run the *configure* file. The log is below: root@ubuntu:~/freesurfer-source/minc-tools/minc-2.1.00# ./configure

Re: [Freesurfer] Funcroi-Table-Sess Error

Hi Doug, Thanks for the help! So, you’re saying that: By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using mri_cor2label, I’ve created volume labels The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels created on the surface. Is this correct? Thanks,

[Freesurfer] Freesurfer - minc lib not found - Ubuntu 12.04

Hi everybody. Could anyone help me please? I've downloaded FreeSurfer source code to compile and install on Ubuntu 12.04, but I've got an error when try to run the *configure* file. The log is below: root@ubuntu:~/freesurfer-source/freesurfer# ./configure --prefix=/root/freesurfer-inst

[Freesurfer] mri_parse_sdcmdir splitting a single series into two?

Hi, I'm running into an issue where the slices from one DICOM series are being parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate series. A few example lines from a scan.out: 6 AR_t.s40.c0 ok 64 64 41 1 7 AR_t.s40.c0 ok 64 64 23 1

[Freesurfer] Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study

Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study University of California, San Diego Several funded postdoctoral positions are available in image analysis method development, including automated cortical- and subcortical segmentation, advanced diffusion

Re: [Freesurfer] FreeSurfer pve correction tool

Dear Bruce, Am I missed the answer of Dr. Greve about the following questions? Is it possible to tell what are the implemented methods for the PET pve correction? and how we can obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)? Many thanks, Mohamed On 26/10/15

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo, the sortData function sorts the rows so that entries from the same subject (in your case same family) are blocked and that within each block the time variable (2nd parameter specifies which column that is in your M matrix, in your case the first =1) is increasing. It is important,

Re: [Freesurfer] FreeSurfer pve correction tool

Hi Mohamed, sorry, I have not fully documented the procedure yet. I've put some notes below doug 1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical