Re: [Freesurfer] Qdec error in analysis

Hi, Thank you for your response. Yes, I checked, and I do have the permission to read the file. Warm Regards Ayushi On Thu, 6 Jul 2017 at 09:42, Douglas Greve wrote: > Do you have read permission to that file? > > On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote: > > Hi, >

Re: [Freesurfer] mri_glmfit error (mri_reshape number of elements)

not sure what is going wrong. Does it work if you do not include the --wls cesvar.nii.gz ? On 6/28/17 12:29 PM, Mcnorgan, Christopher wrote: Hi, I’m running a group-level analysis and have encountered an error that results in a core dump. The first-level analyses were run using the

Re: [Freesurfer] Qdec error in analysis

Do you have read permission to that file? On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote: Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s -qcache" on my data and

Re: [Freesurfer] Raw Cortical thickness values

They are in the ?h.thickness files. You can read them into matlab with read_curv.m or you can convert them to nifti with mri_convert. doug On 8/5/13 5:28 AM, Muhammad Naveed Iqbal Qureshi wrote: Dear Community, I need to know how can I read the numeric cortical thickness values from

Re: [Freesurfer] Average myelination within ROI

The min/max/etc are the voxel wise measures. When you use --accumulate, it sums all the voxels but does not divide by the number of voxels, so you get a number much larger than any one voxel doug On 9/3/14 9:44 PM, SHAHIN NASR wrote: Hi Surfers, I want to measure the average amount

Re: [Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume

So, it looks ok in the volume (using tkmedit) but not on the surface (using tksurfer)? Something is definitely weird. The only thing I can think of is that the surface is not the surface of the subject you think it is. What is your tksurfer command line? What is the subject name in the

Re: [Freesurfer] negative header after preproc-sess

When the nifti standard was adopted, they used a short int to represent the dimensions. Unfortunately, this only allows for a maximum dimension of 32k, which is not big enough for surfaces. So I hacked the FS nifti format to put a -1 as the first dim at which point the FS code will go to

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

The orientation flag was not found. This is an important piece of infomation that should be in the header. Have these dicoms been anonymized? Alternatively, is this may be a newer version of dicom that we are not reading properly yet. On 6/25/17 9:45 PM, 糜超 wrote: Hi, I am preprocessing my

Re: [Freesurfer] GLM fitting for the cortical volume

If you run mris_preproc, then specify --meas volume On 6/24/17 3:10 PM, Ali Radaideh wrote: Dear FS experts, I have managed to run the *glm_fit* on the cortical thickness and area on a group of MS patients. However, i am not sure how to do this on the cortical volume. which file represents

Re: [Freesurfer] Building your own fsaverage

I have not looked at enough to really know. You may get a small boost in power, but it will probably only help if the effects you are looking at are right on the edge of significance. On 6/26/17 1:26 AM, Silas wrote: Dear FreeSurfer team, I'm making a surface based group analysis of 40

Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

there is not an mri_spmregister (there is spmregister). If you have an FA map, then I would use bbregister On 2/25/17 8:03 PM, John Anderson wrote: Hi Doug, thank you for the detailed response. Highly appreciated! Kindly. I want to register FA map to structural T1 image using the command

Re: [Freesurfer] viewing mri_glmfit FDR corrected results

You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr to the FDR you want. Set --subject fsaverage and set the ---hemi. Set --annot aparc. Set --sum to the output summary file. This should give you something similar to the output of mri_glmfit-sim. On 6/29/17 4:29 PM,

Re: [Freesurfer] Question mri_glmfit fwhm smoothing

The fwhm.dat file contains the total amount of smoothness. The data have inherent/endogenous smoothing and then you apply a certain amount, so the total amount is different (more than) the amount you applied. To do correction for multiple comparisons, mri_glmfit-sim needs to know how smooth

Re: [Freesurfer] content of "subjects_dir"

You don't need to move or copy anything. When you run recon-all, it will automatically create a simlink to fsaverage. On 6/29/17 9:04 PM, Schumman Resonance wrote: Dear free surfer community, Silly question here. I note the default "subjects_dir" in freesurfer contains a bunch of

Re: [Freesurfer] Subject with missing fMRI data

We don't have any tools to do imputation. It is possible to have a subject specific mask with the --frame-mask option to mri_glmfit. The frame mask must be the same size as the input (--y) with 1s and 0s to indicate whether a given voxel for a given subject should be included in the model.

Re: [Freesurfer] Recon-all: too many ('s

Can you send the full log file? On 7/3/17 4:03 AM, M del Mar Velasco wrote: Dear all, I am running a recon-all with Freesurfer-Linux-centos6_x86_64-dev-20170330-de24995 and Ubuntu 16.04: recon-all -subjid subject_name -all I am using 0.65m3 images from RM. I get the message ' /Too

Re: [Freesurfer] Fwd: remove skull from gtmseg.mgz

You can change the color to be black or transparent. On 7/5/17 10:53 AM, miracle ozzoude wrote: -- Forwarded message -- From: *miracle ozzoude* > Date: Tue, Jul 4, 2017 at 10:23 AM Subject: remove skull from gtmseg.mgz To:

Re: [Freesurfer] Using multimodal slab input for hippocampus subfield segmentation in FS6

What version of FS are you using? Can you send the recon-all.log file? On 7/3/17 4:35 AM, Frauke Beyer wrote: > Dear experts, > > I am trying to use T2-weighted images (0.5x0.5x1mm) as an additional > scan to a T1-weighted image (0.7x0.7x0.7mm) for hippocampal subfield > segmentation in

Re: [Freesurfer] Still confused by group analysis..

On 6/12/13 7:03 AM, Tudor Popescu wrote: Sorry Doug, wasn't sure whether you'd seen my last reply to this.. On 6 Jun 2013 21:37, "Tudor Popescu" > wrote: Thanks Doug, So if I want to use the study-specific "average" subject

Re: [Freesurfer] recon-all on newborn

Dear Lilla, In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon. If you give me little more details will be easy for me to understand the gap. many thanks Sarbani From:

Re: [Freesurfer] recon-all on newborn

We use a similar pipeline but with different atlases and processing steps for the newborns. Lilla On Wed, 5 Jul 2017, Das S. wrote: > > Thanks for the reply. If you let me know, among the below list of steps of > current recon-all, currently which is not suitable to perform on neonates MRI >

Re: [Freesurfer] error message while using autorecon1

Sourcing FS is something you need to do before running any freesurfer programs in a new shell (terminal). The steps to do this are described here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration The standard method (when using csh) involves running: setenv

Re: [Freesurfer] error message while using autorecon1

I ran "which nu_correct" and it says command not found. What do you mean by the methods used to sourced FS? I am using a linux computing cluster to run FS on. Is this what you mean? Thanks, Colleen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] error message while using autorecon1

After sourcing freesurfer, what comes up if you run the command "which nu_correct"? If it cannot find nu_correct on your path, do you mind telling me the method you use to source FS? Thanks, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Fwd: remove skull from gtmseg.mgz

-- Forwarded message -- From: miracle ozzoude Date: Tue, Jul 4, 2017 at 10:23 AM Subject: remove skull from gtmseg.mgz To: Douglas N Greve Hello Freesurfer, After running the first step of PETsurfer (https://surfer.nmr.mgh.

Re: [Freesurfer] Additional surface area

Hi Michael you need to look in the volume to see what is causing it. I would guess some dura that is being incorrectly included, but you will be able to tell in the slice view cheers Bruce On Mon, 3 Jul 2017, Michael Davies wrote: > > Hello, when inspecting a subject i discovered an

Re: [Freesurfer] error message while using autorecon1

Hi Andrew, The output list includes nu_correct. Thanks, Colleen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject:

Re: [Freesurfer] error message while using autorecon1

Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew From:

[Freesurfer] error message while using autorecon1

Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant

Re: [Freesurfer] Speeding up mri_robust_register with --cost ROBENT

Hi Freesurfers, (Sending again as I think the original may have been lost in the OHBM shuffle) I'm using mri_robust_register to obtain a registration between high resolution (.7mm isotropic) whole-head T1w and T2w images from the same subject. An example command line is: mri_robust_register

Re: [Freesurfer] Convert mgz figure

Hi Lawrence you can convert to any format we support by specifying the proper extention of the output file to mri_convert: mri_convert file.mgz file.nii.gz would create a nifti. I believe you can cfreate a multi-frame tif this way also, if what you want are snapshots of specific slices you

[Freesurfer] To get postings

vittalkor...@gmail.com *Best* *Vittal* ___ 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 whom it is addressed. If

Re: [Freesurfer] Effect of continuous time-varying covariate across time in LME models

Dear Freesurfer's experts, Would anybody have advice concerning my requests in below mail ? Thanks in advance. Best regards, Matthieu 2017-07-01 11:37 GMT+00:00 Matthieu Vanhoutte : > Dear Freesurfer’s experts, > > I would like to test if neuropsychological score

[Freesurfer] sulcus in the orbitofrontal wm

Dear list: We are editing wm and facing a problem we do not know how to solve. In the orbitofrontal wm there is a sulcus that has been fully included into the wm boundary. However there is not wm mask to be erased. I have uploaded the file 40_001 and I would be grateful if could take a look. This

[Freesurfer] Convert mgz figure

Dear FS expert, Is that possible to extract .jpg or .tiff files by using command line? Or convert .mgz file to other format file? If ok , then I can write a program to do this action automatically. Thanks Lawrence ___ Freesurfer mailing list