Hi All,
I was running freesurfer for a patient case of two time points. Will you
suggest to run it as a group, such as one time point as a template and
followed by longitudinal study, discussing atrophy or run these two time
points separately as two individual, running everything such recon-all,
d
Hi,
I am running dti data with trac-all. I followed the command:
trac-all -prep -c /Studies/*/DTI/dmrirc_subject
but it exited with error "*Note: indexing (in both time and space)
starts with 0 not 1! Inputting -1 for a size will set it to the full
image extent for that dimension." *
Before. th
External Email - Use Caution
Hi,
I am trying to use the longitudinal pipeline of the “hippocampal subfields
and nuclei of amygdala”. Keep getting error messages when running it
longitudinal but with no error message running it cross-sectional. I want
to know if there is any way to
CL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list
> *Date: *Thursday, April 30, 2020 at 09:55
> *To: *Freesurfer support list
&g
sias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list
> *Date: *Thu
External Email - Use Caution
Hi,
I run trac-all, the log file has the following endings.
"Queuing post processing stage"
or
"Queuing post processing stage
59 slices processed
All slices processed
/hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh:
line 345:
External Email - Use Caution
Hi,
I have my trac-all up and running with no error with individual subjects
when I set the subject directory to individual subjects.
as follow:
set SUBJECTS_DIR=/*/subjects/SUBJ1
set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2)
set baselist = (SUBJ1_base SUBJ
it create symlinks
> to the dirs of every individual subject (this includes both *.long.* and
> base dirs).
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@ic
u> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Thursday, April 30, 2020 2:22 PM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] trac-all -bedp error
>
>
> External Email - Use Caution
>
> Hi,
>
> I run trac-all, the log f
External Email - Use Caution
Hi,
My trac-all -path exited with error after trying to load BEDPOST parameter
samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong
with my bedpostX from trac-all -bedp? Should I run bedpostX separately
again without trac-all. Th
"
and
same error "Error in kvlReadCroppedImage (line 11)
Error in SegmentSubfieldsT1Longitudinal (line 403)"
Where do I find the Freesurfer license? Here attached the log file.
Thank you so much!
Best,
Qi
On Thu, Apr 30, 2020 at 1:38 PM Zeng, Qi wrote:
> Thank you so much. I w
t and get back to you asap
>
> Cheers,
>
> /Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Ze
research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list
> *Date: *Monday, May 4, 2020 at 12:37
&g
External Email - Use Caution
Hi,
Is it possible to collect all 18 tracts stats into a single file?
Has tried:
"tractstats2table --load-pathstats-from-file paths.txt --overall
--tablefile tractAll.txt"
Path.txt contains all the subjects' 18 paths' full path directory
Error message:
s that contain subjectname, pathwayname,
> and the name of the diffusion measure that you want.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
>
External Email - Use Caution
Hi,
I was running longitudinal trac-all. After the 3rd step -path was finished,
I found that multiple pathways were missing (e.g. fminor). I traced back,
realizing outputs from its first step trac-prep were missing corresponding
pathways in SUBJ_base/d
External Email - Use Caution
Hi,
I conducted longitudinal segmentation of both hippocampus and amygdala from
running segmentHA_T1_long.sh. But is it possible for me to segment only the
hippocampus region "mgz" from the stored
[lr]h.hippoAmygLabels-T1.long.v21.mgz ?
Best,
Qi
--
t;
> mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300
> [lr]h.hippoLabelsNoAmyg-T1.v21.mgz
>
>
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
range and the hippocampal in
> the 200s. Feel free to use eg 4129 next time!
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on b
t; CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Zeng, Qi" <
> qi.z...@icahn.mssm.edu>
> *Reply-To: *Freesurfer support list
> *Date: *Friday, June 5, 2020 at 16:02
> *
External Email - Use Caution
Hi All,
I am a little confused with the stats output. So seg/aparc are cortical
white /grey matter and wmparc are subcortical white matter. Is that correct?
Best,
Qi
___
Freesurfer mailing list
Freesurfer@nm
seg)
> parc is usually a surface-based segmentation (like lh.aparc.annot)
> unfortunately, I misnamed "wmparc". It is a volume-based segmentation that
> incorporates surface-based information
>
> On 6/12/2020 3:12 PM, Zeng, Qi wrote:
>
> External Email - Use C
, Jun 15, 2020 at 10:28 AM Douglas N. Greve
wrote:
> I'm not sure what you mean. Are you looking for a single file that
> contains all the info? If so, the answer is no, we do not output such a file
>
> On 6/13/2020 5:10 PM, Zeng, Qi wrote:
>
> External Email - Use C
External Email - Use Caution
Hi,
I have a question about how to handle outliers in aparc, aseg and tracula
results? Usually, each subject has one result regarding one measurement and
I detect and remove outliers using barplot. However, for results in
freesurfer, we have multiple o
External Email - Use Caution
Hi,
When conducting group-level analysis, for example comparing volumetric
differences or tractography FA across subjects between groups. How we
correct for the size of the brain when comparing volumetric differences or
correct for the whole brain FA?
ing it in your
> analysis.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 11:44 AM
>
o ask that requires it.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 10:03 PM
> *To:* Fr
’t mean that the FA is
> higher *everywhere* in the brain, so it's not a global effect in the way
> that a bigger brain would be a global effect. I hope this makes sense!
> ------
> *From:* Zeng, Qi
> *Sent:* Monday, August 31, 2020 10:57 PM
> *To:* Yendiki,
External Email - Use Caution
Hi,
Where is the nifti output stored from running trac-all preprocess? Is
it dmri/dwi.nii.gz? Is there an additional step segment this nifti file
into the grey matter and white matter for later tensor-fitting?
Best,
Qi
External Email - Use Caution
Hi,
I was conducting a longitudinal DTI analysis. However, MRI and DTI brain
scans were scheduled at different time frames. Should I be concerned that
for example MRI was taken at 9/1/2006 and nearby DTI was taken on 10/1/2007
or 10/1/2009, which may r
External Email - Use Caution
Hi,
Is it possible to use Freesurfer to extract global voxel-wise cortical
thickness and subcortical volume?
Thank you so much!
Best,
Qi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mai
External Email - Use Caution
Hi Freesurfer experts,
Are the steps for processing DTI scan the same for single and multiple
shells? for example, both via -prep, -bedp, -path.
Thank you so much!
Best,
Qi
___
Freesurfer mailing list
Freesu
External Email - Use Caution
Hi,
I run both recon-all and trac-all for each subject. Where are the original
T1 and DTI data stored in the output files?
Thank you so much!
Best,
Qi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.e
External Email - Use Caution
Hi Experts,
I am running the last step (-long) for a longitudinal analysis, However,
encountering an error message saying: "error: ERROR: number of asegs and
norm volumes do not match" for all the subjects I run this time. A similar
problem has been re
External Email - Use Caution
Hi Experts,
I understand there is surface-based group analysis in Freesurfer, which is
for thickness, curvature, volume and etc. Is there a group analysis for DTI
tracula results? Any links to recommend to conduct the analysis?
Thank you so much!
Best
rf.mgz.
>
> On 4/16/2021 4:35 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Experts,
>
> I am running the last step (-long) for a longitudinal analysis, However,
> encountering an error message saying: "error: ERROR: number of asegs and
> norm volume
External Email - Use Caution
Hi Douglas,
They each contained mri/norm.mgz.
Best,
Qi
On Tue, Apr 20, 2021 at 10:10 AM Douglas N. Greve
wrote:
> and do they each have a norm.mgz?
>
> On 4/19/2021 4:11 PM, Zeng, Qi wrote:
>
> External Email - Use Cauti
External Email - Use Caution
Hi Freesurfer experts,
I've done running a longitudinal analysis pipeline for individuals in 3
groups. Now, I need to get prepared for QDEC group analysis. I cp all
groups of individuals to the same directory and each subject contains one
base and mult
External Email - Use Caution
Hi Experts,
I've finished my run of generating volumetric and Tracula data for
subjects. I was wondering if there is a way of displaying
significant regions that correlate with clinical traits and also by groups.
If there is a page describing this fun
External Email - Use Caution
Hi Experts,
If I want to analyze and visualize baseline and follow-up for an individual
subject's change (before-after & after-before). Should I treat it as a
cross-sectional analysis for a group analysis?
Best,
Zeno
_
External Email - Use Caution
Hi Experts,
After completing long_mris_slopes to get the rate of change and then
concatenating them into one.mgh file for group analysis (mris_preproc). I
am finally getting to mris_glmfit. Got a couple of questions along the way.
1). if I conducted lo
External Email - Use Caution
Hi Freesurfer Experts,
Just a follow-up on the questions I asked last week and tested if the
questions get through to the list. Thanks for your help in advance!
Best,
Zeno
On Fri, Oct 29, 2021 at 10:39 PM Zeng, Qi wrote:
> Hi Experts,
>
&
External Email - Use Caution
Hi Freesurfer experts,
Here, I want to design a simple group comparison (two levels: Case vs.
Control) and also count for 4 covariates (two continuous and two
categoricals). However, the GLM model cannot recognize my discrete
variables. What do you sug
ached FSGD file below.
Thank you so much for the help!
Best,
Zeng
On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve
wrote:
> please send your command line and full terminal output as well as the fsgd
> file
>
> On 11/10/2021 5:12 PM, Zeng, Qi wrote:
>
> Exter
s numbers
> You have listed Gender and Race as strings, they have to be numbers (eg,
> 1, 2)
> You probably want to have these be discrete variables instead of continuous
>
> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
&g
, Nov 10, 2021 at 6:38 PM Douglas N. Greve
> wrote:
>
>> Did you read the error message? It says:
>> Variable 2 has character string Female
>> Variables should be continuous numbers
>> You have listed Gender and Race as strings, they have to be numbers (eg,
>> 1, 2)
&
On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> If to set up the FSGD as below, is my design matrix for case and control
> comparison as "1 -1 1 -1 1 -1 1 -1 0 0" ?
>
> GroupDescriptorFile 1
> Title MyStud
External Email - Use Caution
got you, thanks
Best,
Zeng
On Thu, Nov 11, 2021 at 4:06 PM Douglas N. Greve
wrote:
> For DODS you would add 16 zeros (8 classes times 2 continuous variables)
>
> On 11/11/2021 4:00 PM, Zeng, Qi wrote:
>
> External Email - U
discrete as covariates?
Best,
Zeng
On Thu, Nov 11, 2021 at 4:07 PM Zeng, Qi wrote:
> got you, thanks
>
> Best,
> Zeng
>
>
>
> On Thu, Nov 11, 2021 at 4:06 PM Douglas N. Greve
> wrote:
>
>> For DODS you would add 16 zeros (8 classes times 2 continuous variable
External Email - Use Caution
Hi Experts,
My tracula completed with no error. So I was trying to view the fa.nii with
the following command:
freeview -v mri/brain.mgz mri/orig.mgz
mri/wmparc.mgz:colormap=lut:opacity=0.2
dmri/dtifit_FA.nii:reg=touch/rusage.mri_ca_register.dat:color
External Email - Use Caution
Sorry for the trouble, I seemed to find the registration matrix located in
xfms/anatorig2diff.bbr.dat. Is that one correct?
Best,
Jackie
On Mon, Nov 22, 2021 at 12:36 PM Zeng, Qi wrote:
> Hi Experts,
>
> My tracula completed with no er
External Email - Use Caution
Hi,
If I want to freeview fully segmented grey matter, white matter, and
Tracula outputs, are the following commands correct to the request?
# to visualize the segmented cortical outputs
freeview -v mri/aparc+aseg.mgz
Question: why is one hemisphere b
= L1
> RD = (L2+L3)/2
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, November 22, 2021 5:24 PM
> *To:* Freesu
External Email - Use Caution
Hi,
I got a couple of questions regarding group analysis of tracula with a
longitudinal pipeline, freeview output heatmap key, and pair analysis's
fsgd & correction analysis.
1). I followed FsTutorial/TraculaStatistics - Free Surfer Wiki (harvard.edu)
External Email - Use Caution
Hi,
I saw the same question has been asked and no answer was provided:
I run
"mri_cor2label --c fsaverage/mri/aseg.mgz --id 4 --l
fsaverage/label/Left-Lateral-Ventricle.label --surf fsaverage lh"-
to hopefully extract lateral ventric
External Email - Use Caution
Hi experts,
Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after
correction for B0 inhomogeneities, eddy current, and head motion? and
dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and
dmri/bvals and dmri/bvecs are r
quot;bet" (brain
extraction)
> and dmri/nodif_brain_mask.nii is derived from aparc+aseg_mask.nii.gz
which contains T1 information.
Because in fsl, nodif_brain_mask is named for "bet binary brain mask".
Best,
Qi
Best,
Qi
On Fri, Apr 22, 2022 at 3:25 PM Zeng, Qi wrote:
> Hi exper
External Email - Use Caution
Hi,
I was trying to demonstrate my findings by visualizing a significant tract
and a ROI at the same time on a single template or volume, for example,
left UNC and orbitofrontal overlaid on the T1-weighted.nii. However, I only
saw Freeview on tractogra
External Email - Use Caution
Hi Freesurfer scholars,
The output of recon-all "aseg.stats" file contains information on volume
and intensity statistics of each segmentation of subcortical brain regions.
May I ask what is this intensity measurement (e.g. intensity mean)? How is
it d
External Email - Use Caution
Hi Freesurfer experts,
If I just want to normalize, register, and segment the T1-weighted images
to the GM, WM, and CSF tissues, can certain steps be skipped from
recon-all, such as the inflation process? What is the output for the
segmentation of GM,
60 matches
Mail list logo
