[Freesurfer] what command can be used to template .vtk file to fsaverage5 space?

[1248742467]

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Hello, what command can map VTK file to fsaverage5 space? I want its vertex 
number to be 10242. If you know, please give me an example.
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Re: [Freesurfer] mri_segstats question

[RENXI LI]

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The WM was cropped out by applying a grey-matter mask in SPM, and I am trying 
to extract non-zero voxels with mri_segstats.

Best,
Renxi

> On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D. 
>  wrote:
> 
> I don't understand why WM was cropped out. What command were you trying 
> to use?
> 
> On 11/18/2020 2:39 AM, RENXI LI wrote:
>> External Email - Use Caution
>> 
>> Hi Freesurfer experts:
>> 
>> I am trying to extract the mean-time series from the functional image using 
>> mri_segstats. However, the cerebral white matter signals were cropped out in 
>> my functional images, and the regions that I am trying to extract signal 
>> from are close to the cerebral white matter that some voxels at the boundary 
>> may not contain any signals. Is there any arguments in mri_segstats that I 
>> can use to only extract voxels that has non-zero time-series?
>> 
>> Best,
>> Renxi
>> 
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Re: [Freesurfer] extracting mask for basal ganglia, deep grey, and centrum semiovale

[Greve, Douglas N.,Ph.D.]

We don't have a centrum semiovale label in FS. You could try using the 
(Left,Right)-UnsegmentedWhiteMatter in the wmparc.mgz

On 11/27/2020 9:28 AM, miracle ozzoude wrote:

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Hello Experts,

I did like to create a mask for basal ganglia, deep grey matter, and centrum 
semiovale. I know how to extract the mask for the first 2 (using aseg.mgz) 
however, how do I extract the last one. What mask should I use to extract the 
centrum semiovale? I don't want to include the cerebellar white matter.

Thanks.

Best,
Paul



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Re: [Freesurfer] Mean Curvature

[Greve, Douglas N.,Ph.D.]

I don't know. I've never seen this type  of analysis. I think with and without 
would be valid analyses, but they would be answering different questions, so, 
as the scientist doing the study, it is more up to you.

On 11/27/2020 8:56 AM, Letitia Schneider wrote:
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Re: [Freesurfer] mri_segstats question

[Greve, Douglas N.,Ph.D.]

what is your command line?

On 11/29/2020 2:55 PM, RENXI LI wrote:
>  External Email - Use Caution
>
> The WM was cropped out by applying a grey-matter mask in SPM, and I am trying 
> to extract non-zero voxels with mri_segstats.
>
> Best,
> Renxi
>
>> On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D. 
>>  wrote:
>>
>> I don't understand why WM was cropped out. What command were you trying
>> to use?
>>
>> On 11/18/2020 2:39 AM, RENXI LI wrote:
>>>  External Email - Use Caution
>>>
>>> Hi Freesurfer experts:
>>>
>>> I am trying to extract the mean-time series from the functional image using 
>>> mri_segstats. However, the cerebral white matter signals were cropped out 
>>> in my functional images, and the regions that I am trying to extract signal 
>>> from are close to the cerebral white matter that some voxels at the 
>>> boundary may not contain any signals. Is there any arguments in 
>>> mri_segstats that I can use to only extract voxels that has non-zero 
>>> time-series?
>>>
>>> Best,
>>> Renxi
>>>
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Re: [Freesurfer] monkey atlas D99

[Greve, Douglas N.,Ph.D.]

Use mri_label2vol to map the segmentation into the fMRI space, then use 
mri_segstats using the --avgwf option to get time courses. Run it with --help 
to get examples

On 11/26/2020 9:16 AM, Francesca Strappini wrote:

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Dear FreeSurfer experts,

I'm trying to use the monkey atlas D99. First, I registered the segmentation 
atlas to the monkey anatomy through bbregister. Now, I need to resample the 
segmentation to the functional data and extract the mean value from each 
functional run using the ROIs contained in the segmentation as masks. I suppose 
I should mri_segstats but I'm not sure how. Any suggestion?

Thank you
Francesca


--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: 
francesca.strapp...@weizmann.ac.il



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Re: [Freesurfer] error: MatrixMultiply: m1 is null {Disarmed}

[Greve, Douglas N.,Ph.D.]

Not in FS. Try using dcm2niix

On 11/26/2020 5:07 AM, John Papatriantafyllou wrote:

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Hi freesurfer exps,
last year a recieve dicom 3d as one file (300 dicoms one file)
Is there any program to unpack them or any other way to recon all
John


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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

No, you'll have to add it as a covariate. Or you can add --etiv when you run 
mris_preproc and it will divide the maps by the eTIV

On 11/25/2020 3:23 PM, Sara Lyn wrote:

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Hi Freesurfer experts,

I'm doing a surface based volume analysis and wanted to know if there was a 
flag to regress out eTIV in the model.

Thank you



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Re: [Freesurfer] Mean Curvature for whole hemisphere

[Greve, Douglas N.,Ph.D.]

No, probably just an oversight

On 11/25/2020 10:06 AM, Josue Luiz Dalboni Da Rocha wrote:
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Re: [Freesurfer] PETSurfer voxelwise statistic

[Greve, Douglas N.,Ph.D.]

Traditionally, MG analysis is only run on GM. In principle, it is possible to 
run it on WM, but we don't offer that as an option.

On 11/25/2020 8:16 AM, Boris Rauchmann wrote:

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Dear all,

How can I run a voxelwise statistic using grey and white matter uptake? 
mgx.ctxgm.nii.gz and the other files in output all only include gm as I 
understand.

My goal is to run whole brain volume-based analysis. Like in this example for 
subcortical analysis:

mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta
--tal --talres 2  --o subctxgm.mni305.2mm.sm00.nii.gz

Thanks,
Boris





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Re: [Freesurfer] Splitting a label region?

[Greve, Douglas N.,Ph.D.]

Try mris_divide_parcellation
Run with --help to get docs

On 11/25/2020 1:57 AM, Hyon, Justin J. wrote:
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>
> Hello,
> I am wondering whether there is a way to split a labeled region in a volume 
> into 2 labels, perhaps by using the Freeview gui? I just need to roughly 
> split one region generated via one of the default atlases into 2 custom 
> labels. I tried using the tools in Freeview, but I can only seem to edit 1 
> layer of the volume at a time.
> Thank You!
>
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Re: [Freesurfer] group analysis

[Greve, Douglas N.,Ph.D.]

For starters, you need to have four classes, HC-Male, HC-Female, CMT-Male, 
CMT-Female and not use gender as a variable. Try that. I would also normalize 
the age and thickness

On 11/24/2020 12:04 PM, Ambulatorio SNA FEDERICO II wrote:

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Dear Freesurfer team,

I'm running a group analysis where I'd like to compare myelination between two 
groups regressing out cortical thickness, age and sex.
My FSGD file is:
GroupDescriptorFile 1
Title Func
Class HC
Class CMT
Variables  Age gender
Input fs_VF HC  46 Female
Input fs_RF HC 24 Female
...

My group.diff.mtx is:
1 -1 0 0 0 0 0

My command line:
 mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd 
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf 
fsaverage rh --cortex --glmdir 
rh_allbrain_t1t2_group_thickness_age_gender.glmdir

But unfortunately I get this wrong message:
RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd 
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf 
fsaverage rh --cortex --glmdir 
rh_allbrain_t1t2_group_thickness_age_gender.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=146.140350 (col 3)
 The scale is much different between columns 5 and 3, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same


Can you please help me?

Thank you very much
Raf



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Re: [Freesurfer] Manual ROIs in PETSURFER

[Greve, Douglas N.,Ph.D.]

It is, but it can be either easy or hard. The easy way is to draw it on 
gtmseg.mgz and add an entry into gtmseg.ctab. Probably, you should copy the 
gtmseg.{mgz,ctab} to a new file and edit that. Otherwise, you can edit, eg, 
apas+head.mgz, and pass that to gtmseg with the --head option. At some point, 
the the ctab will need to be updated or gtmseg will fail. We will be updating 
this part to make it easier in the next year.

On 11/23/2020 4:27 PM, Jessica Cooperrider wrote:

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Hello,

I would like to draw a volume of interest on T1 images and then evaluate 
metabolism changes in this region. Is this possible to accomplish using 
PETSURFER?

Thank you for your time,
Jess



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Re: [Freesurfer] mri_surf2surf (and mri_preproc) clarification

[Greve, Douglas N.,Ph.D.]

I think that would be ok, but I would run this instead

mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type 
curv --cortex --trgsubject fsaverage5  --trgsurfval ./mgh/1001_lh_fs5_thick.mgh 
--trg_type mgh –fwhm-trg 10



On 11/23/2020 4:11 PM, Daniel Leopold wrote:

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Dear Freesurfer experts,

The mri_surf2surf example 1 specifies that lh thickness is resampled onto the 
7th order icosahedron. Does it place the lh.thickness curv into freesurfer 
space, or is it still in the subject's native space (i.e., pre-transformation 
to the fsaverage template)?

I used a similar process to downsample subjects' thickness to fs5 resolution, 
which I then concatenated and used as input for PALM. What I'm now wondering is 
whether results may be due to misalignment between individual subjects because 
they were not transformed to the fsaverage template and space. Do the inputs 
below (-srcsurfval) need to be thickness.fsaverage.mgh (already mris_preproc'd 
in the recon-all pipeline) instead?

mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type 
curv --cortex --trgsubject ico --trgicoorder 5 --trgsurfval 
./mgh/1001_lh_fs5_thick.mgh --trg_type mgh –fwhm-trg 10

**Note: My apologies if this re-posts, but it doesn't seem like my initial 
submission went through**


With gratitude,
Dan



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Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

[Greve, Douglas N.,Ph.D.]

If you want a cluster table, then you will have to run mri_surfcluster on the 
output of the conjunction. Run it with --help and write back if you need more 
info

On 11/21/2020 10:03 AM, Paula Maldonado wrote:

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Dear Douglas,

Could you please tell me where can I find the cluster table?

Thank you,
Best regards,

Paula

Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

There is not a summary table, it is just a map. Do you want a cluster table?

On 11/10/2020 11:26 AM, Paula Maldonado wrote:

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Thanks for your reply, that worked. Can you please tell me where I can find a 
summary table of the activated regions resulting from the conjunction analysis?

Best regards,

Paula




Il giorno 27 ott 2020, alle ore 22:50, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

You would just run mkcontrast-sess, eg, if your four conditions are
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
-a 4
If you want it reversed, then just reverse the a's and c's

On 10/23/2020 4:39 AM, Paula Maldonado wrote:
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Dear experts,
I am running an fMRI experiment in which I have four conditions: two main 
conditions (condition A and condition B) and two respective control conditions 
(condition Acontrol and condition Bcontrol).
I would like to create a map showing significantly greater activity for 
condition A relative to condition B, after subtracting out the activity for the 
respective control conditions. In other words, I would like to perform the 
following contrast:
(condition A - condition A control) - (condition B - condition B control)
Then I would like to have a map that shows the reverse contrast too:(condition 
B - condition B control) - (condition A - condition A control).

How do I do that?To obtain the first map: (condition A - condition A control) - 
(condition B - condition B control) I have tried with the mergecontrasts-sess 
function with the -conjunction flag and the OR option as detailed below:
mergecontrasts-sess -mergedcontrast conjres -conjunction or -analysis 
analysisname -map sig -space sph -isxavg fixed -contrast Contrast1 2 pos 0 
-contrast Contrast 2 pos 0 -s sessionsfMRI/Sub01/bold -hemi lh

where Contrast1= (condition A - condition A control) and Contrast2= (condition 
B - condition B control)
however the map I get is exactly the same as (condition A - condition A 
control), as if subtracting out Contrast 2 had no impact on the map.

Thanks,

Paula



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Re: [Freesurfer] PETSurfer

[Greve, Douglas N.,Ph.D.]

One way you can do it is to specify all the GM ROIs with --rescale Id1 Id2 ...
Otherwise, you can run fscalc, eg,

fscalc mgx.ctxgm.nii.gz div `cat global.gm.dat ` -mul 100 -o 
mgx.ctxgm.rescaled.nii.gz



On 11/20/2020 11:44 AM, Boris Rauchmann wrote:

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Dear all,

How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean 
intensity using PETSufer? Is there a command to use in mri_gtmpvc like 
--rescale X?
I know that I can find the mean in  global.gm.dat and I can use that value for 
scaling the atlas based results in gtm.stats.dat but how can I easily scale the 
image?

Thanks,
Boris






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Re: [Freesurfer] Time required to run permutations

[Greve, Douglas N.,Ph.D.]

This might be a bug with the --bg option when 1 is specified. Try it without 
--bg or try it with 2 or more threads

On 11/20/2020 10:20 AM, Basavaraju, Rakshathi wrote:
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Re: [Freesurfer] MNI Coordinates from the Destrieux Atlas and aseg.stats ROIs

[Greve, Douglas N.,Ph.D.]

It is probably easier to just run recon-all on the mni152, then use 
mri_segcentroids on aparc.a2009s to extract the centroids

On 11/20/2020 2:50 AM, Hengameh Marzbani wrote:

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Hello Freesurfer developers,




For the purpose of reporting ROIs in my article, I need a list of X Y Z 
coordinates in MNI space for all the labels in the Destrieux atlas. I came 
across a previous post with the following steps:

Step 1:
 mri_annotation2label --subject fsaverage --hemi lh --annotation
 aparc.a2009s --outdir ~/myproject/processed/tmp

Step 2:
mri_surfcluster --in ~/myproject/processed/fsaverage/surf/lh.thickness --clabel 
lh.G_pariet_inf-Supramar.label --sum 
~/myproject/processed/tmp/sum.lh_G_pariet_inf-supramar  --centroid --thmin 0 
--hemi lh --subject fsaverage --nofixmni





Q1: All the ROIs appeared to have identical MNI coordinates. what should I do?

Q2: For reporting the list of X Y Z coordinates in MNI space for all the labels 
in aseg.stats ROIs, What should I change?




Thank you in advance,
Best regards,
Hengameh




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Re: [Freesurfer] -openmp vs -threads, -parallel options in recon-all

[Greve, Douglas N.,Ph.D.]

I think it will be threads.

On 11/19/2020 10:21 PM, d m wrote:

External Email - Use Caution

Thanks.

Just to confirm, the openmp reflects threads and not cores? In other words, on 
we have a 4 core machine with hyperthreading, so with 4 cores we have 8 threads 
available.

In that scenario, would the -openmp 4 option reflect 4 cores/8 threads or just 
4 threads.

Thanks again.

d.m.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Wednesday, November 18, 2020 6:09 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] -openmp vs -threads, -parallel options in recon-all

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Re: [Freesurfer] Issue with custom label

[Greve, Douglas N.,Ph.D.]

If you want the parahippo label on the surface, then convert the lh.aparc.annot 
to labels with mri_annotation2label. Run with --help to get examples

On 11/19/2020 11:57 AM, Catherine Tallman wrote:

External Email - Use Caution

Hello,

After running mri_vol2label I created a custom label named test.label. When I 
try to load the label onto lh.pial, I receive the following error: "Could not 
load label from ". The file is saved within the path folder itself. 
Within the terminal I receive the warning "label has not been mapped to 
surface". I was wondering what might be causing this issue? Attached is the 
label file.

mri_vol2label --c mri/aparc+aseg.mgz --id 1016 --l 
label/lh.parahippocampal.label

Thank you,
Catherine
--

Catherine Tallman, M.A.
Graduate Student
CNS Laboratory of Memory and Brain
University of California, San Diego



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Re: [Freesurfer] Group Analysis

[Greve, Douglas N.,Ph.D.]

By "volume" do you mean a surface-based, vertex-wise measure of volume or do 
you mean volume of an ROI?

On 11/19/2020 11:46 AM, Mora, Jocelyn S. wrote:
Hi Sara,

You may want to use asegstats2table. Follow these links to learn more about 
mris_preproc, mri_glmfit, and asegstats2table:

http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit?highlight=%28asegstats%29

https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table?highlight=%28asegstats%29

Best,
Jocelyn

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Sara Lyn 
Sent: Wednesday, November 18, 2020 6:37 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: [Freesurfer] Group Analysis


External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri 
surf2surf using the measure volume and unsure of how to go about it since the 
wiki page talks about thickness only. I would appreciate any help.

Best,
Sara



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Re: [Freesurfer] extracting beta coefficients and p-values {Disarmed}

[Greve, Douglas N.,Ph.D.]

Yes, that is correct

On 11/19/2020 11:43 AM, Batool Rizvi wrote:

External Email - Use Caution

Hi Dr. Greve,
Sorry to bring this back up, but I didn't fully understand how to calculate the 
variance in order to get the confidence intervals for each covariate, so I 
wanted to double check the steps.
A colleague in the lab is helping me to derive the variance using Matlab, and 
just wanted to make sure of the formula I would use:

variance of B = rvar.mgh * inverse(transpose(Xg.dat)*(Xg.dat))

Is this the correct formula to derive variance in Matlab?

Thanks again for your help,
Batool


On Fri, Oct 9, 2020 at 5:46 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
You can standardize them yourself. rvar.mgh is the residual variance and Xg is 
the design matrix. Between those and the beta values, you can standarize the 
betas

On 10/7/2020 3:39 PM, Batool Rizvi wrote:

External Email - Use Caution

Hi Dr. Greve,

Thank you for your response! Not sure if you already addressed this, but my 
second question was whether there is a way to derive the (95%) confidence 
intervals for my covariates that were included in the mri_glmfit analyses?

Thanks again!
Batool

On Wed, Oct 7, 2020 at 7:31 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


On 10/6/2020 4:26 PM, Batool Rizvi wrote:

External Email - Use Caution

Hi,

I had a couple additional questions related to this topic.

1. The beta-coefficients I derived from using the mri_segstats command with the 
input beta.mgh, are these values unstandardized?
Yes, that have not been standarized

2. Just wondering, is there a possible way to also derive 95% confidence 
intervals for my covariates that were included in the mri_glmfit analyses?
You can standardize them yourself. rvar.mgh is the residual variance and Xg is 
the design matrix. Between those and the beta values, you can standarize the 
betas

Thanks so much for your help!
Batool

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Re: [Freesurfer] Mean thickness estimation

[Greve, Douglas N.,Ph.D.]

Are you talking about outliers across subject? Or across region? I would just 
take the FS-supplied value instead of averaging the regions.

On 11/19/2020 2:14 AM, Stephanie K wrote:

External Email - Use Caution

Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

Thank you!



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Re: [Freesurfer] eddy_correct with DTI {Disarmed}

[Greve, Douglas N.,Ph.D.]

Can you upgrade to 6 or  higher?

On 11/13/2020 1:32 PM, Wei Shao wrote:

External Email - Use Caution

Hi Douglas

I think it's 5.0.11

[weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0
To initialize FreeSurfer,
do (sh, ash, ksh, and bash)
  source $EBROOTFREESURFER/FreeSurferEnv.sh
or (csh, tcsh)
  $EBROOTFREESURFER/FreeSurferEnv.csh

[weishao@gra-login2 ~]$ module load fsl
[weishao@gra-login2 ~]$ which fsl
/cvmfs/MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/fsl
[weishao@gra-login2 ~]$

Best,
Wei

On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
What version of FSL are you using?

On 11/10/2020 12:19 AM, Wei Shao wrote:

External Email - Use Caution

Hi, Freesurfer team,

My name is Weishao, Here is a problem that bothers me a lot I try to run DTI. I 
have loaded the FSL module and use the most recent version of Freesurfer. it's 
appreciated if someone can help. Thanks.

Here is the script.

dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval 
sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec
--i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
--s /home/weishao/scratch/rawdata/sub-AVP6176/
--o /home/weishao/scratch/rawdata/sub-AVP6176/

Here is feedback

-rw-r- 1 weishao weishao 49041968 Sep  9 11:41 
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
INFO: SUBJECTS_DIR is 
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects
dt_recon logfile
Tue Oct 27 16:19:28 EDT 2020
VERSION dt_recon 7.1.0
setenv SUBJECTS_DIR 
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects
cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon --b 
sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval 
sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i 
sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s 
/home/weishao/scratch/rawdata/sub-AVP6176/ --o 
/home/weishao/scratch/rawdata/sub-AVP6176/
gra95
weishao
/cvmfs/MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct
ECRefTP 0
#@#---
Converting input
Tue Oct 27 16:19:28 EDT 2020
cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi
mri_convert 
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
 /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
mri_convert 
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
 /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
reading from 
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz...
TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999608, 0.017447, -0.021891)
j_ras = (0.0104682, 0.958258, 0.285714)
k_ras = (-0.0259621, -0.285373, 0.958065)
writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz...


#@#---
Eddy/Motion Correct
Tue Oct 27 16:19:44 EDT 2020
cd /scratch/weishao/rawdata/sub-AVP6176/ectmp
eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz 
/scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0
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"secure-web.cisco.com" claiming to be 
soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct:
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Re: [Freesurfer] PET image format

[Greve, Douglas N.,Ph.D.]

Sorry, we don't have any tools to convert from PET formats. Not sure where to 
go for that ...

On 11/19/2020 8:27 AM, Marina Fernández wrote:

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Dear experts!

I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I 
would like to convert the images to nifti format to start processing the data.
What function can I use to convert the images?
How can I check that the left-right orientation doesn't flip?

Thank you in advance!
Marina.




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Re: [Freesurfer] mris_pmake error - freadFloat: fread failed

[Greve, Douglas N.,Ph.D.]

It is mris_smooth. Look in the recon-all.log or recon-all.cmd for the exact 
command

On 11/13/2020 10:15 AM, Nasr, Shahin,Ph.D. wrote:
Good morning Doug,
  I can load ?h.white and rh.smoothwm but not lh.smoothwm to freeview. I 
can even load lh.smoothwm.nofix. So apparently, that is the corrupted file.  
So, would you tell me how to regenerate the lh.smoothwm without redoing the 
whole recon?

Thanks

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Friday, November 13, 2020 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] mris_pmake error - freadFloat: fread failed

Can you open the smoothwm with another application? Eg, mris_info or freeview -f

On 11/12/2020 9:52 AM, Nasr, Shahin,Ph.D. wrote:
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Re: [Freesurfer] Group Analysis

[Greve, Douglas N.,Ph.D.]

Make sure that --meas volume was passed to  mris_preproc was passed (this is 
the usual way you would do this) in which case it makes a jacobian correction. 
The only other thing to do would be to correct for intra-cranial volume. If you 
have 7.X, you can just add --etiv to mris_preproc

On 11/18/2020 6:37 PM, Sara Lyn wrote:

External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri 
surf2surf using the measure volume and unsure of how to go about it since the 
wiki page talks about thickness only. I would appreciate any help.

Best,
Sara



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Re: [Freesurfer] RHEL 7 and tkmedit {Disarmed}

[Greve, Douglas N.,Ph.D.]

We certainly cannot guarantee that tkmedit will work as that is a pretty old 
program. Try using tkmeditfv in a newer version of FS. It will be ok as long as 
the analysis (eg, recon-all, preproc-sess, etc) was done in 5.1

On 11/18/2020 12:00 PM, Tracy Riggins wrote:

External Email - Use Caution

Dear Freesurfer Gurus
We just upgraded our server to RHEL 7.  However, we want to do some white/pial 
edits on some brains using Freesurfer 5.1.0.  We know this is an old version, 
but we are combining some new data with a lot of old data that had been 
processed before in 5.1.0 and ... we want to use the old version.

However, when using tkmedit the error below was received.

Can you help?
Thanks in advance,
Tracy

===
ERROR: A segfault has occurred. This is not your fault,
  : but is most likely an unrecoverable error and has
  : made the program unstable.
  :
  : Please send the contents of the file .xdebug_tkmedit
  : that should be in this directory to 
freesurfer@nmr.mgh.harvard.edu
  :
  : Now exiting...

Contents of the the file .xdebug_tkmedit here:

tkmedit started: Wed Nov 18 10:50:06 2020

/cell_root/software/freesurfer/5.1.0/sys/tktools/tkmedit.bin SLP003_practice_KK 
brainmask.mgz -aux wm.mgz -surfs

$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $
Set user home dir to /export/data/seahorse_ncdl/SLP/data/white_pial_practice
Set subject home dir to 
/export/data/seahorse_ncdl/SLP/data/white_pial_practice//SLP003_practice_KK

Segfault
Importing volume with MRIread
xDebug stack (length: 5)
  04: Volm_ImportData( this=0x27f57890, 
isSource=/export/data/seahorse_ncdl/SLP/data/white_pial_practice//SLP003_practice_KK/mri/brainmask.mgz
 )
  04: Importing volume with MRIread
03: LoadVolume( iType=0, isName=brainmask.mgz, ibConform = 0 )
03: Reading data into volume
  02: ParseCmdLineArgs( argc=6, 
argv=/cell_root/software/freesurfer/5.1.0/sys/tktools/tkmedit.bin )
  02: Loading volume brainmask.mgz
01: main()
01: Parsing command line arguments
  00:
  00:

]
--
Tracy Riggins, Ph.D.
Associate Professor
Secretary, Cognitive Development Society
Department of Psychology
4094 Campus Drive
Biology/Psychology Building Room 2147J
University of Maryland
College Park, MD 20742
(301) 405-5905
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Pronouns: she/her/hers




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Re: [Freesurfer] calculating hemisphere total grey matter volume

[Greve, Douglas N.,Ph.D.]

We use partial volume correct. Maybe that is the problem. What version 
of FS are you using?

On 11/18/2020 10:37 AM, Vicente Ferrer wrote:
>  External Email - Use Caution
>
> Hello Freesurfer,
>
> Once I had run reconall, I tried to calculating left hemisphere total grey 
> matter volume and right hemisphere total grey matter volume by doing the sum 
> of:
> TGM_left=lhcortexvol + Left-Cerebellum-Cortex + (Left-Thalamus-Proper + 
> Left-Caudate + Left-Putamen + Left-Pallidum + Left-Hippocampus +Left-Amygdala 
> +Left-Accumbens-area +Left-VentralDC)
> using the volumes values of the aseg.stats file. I did it like this because 
> of the definitions of TGM in this webpage: 
> https://secure-web.cisco.com/18pk-Ax0hgeQLjPCil_KNGcr0ZuCL3RBLq8NqkvLiWHU5VUuiUJaOV52GhfgAFzPXuKyXv3OUSjgFM-YHEKavejpBfKj58Pep5TTckz0Jl3Td1z2zeHjXA79b84MWTgc1vEfGiXx_Z2b3f9TPeN2KNroaOGb3GR4I8_PiH42P7pcpeHZmAVC_0XgdS7yUdIYD9Q-2YJZ9937_sKFs8lz_iIvJatyvfuFZekY3YmxFPV1308K7BeSLplhIHvUJV2AaV3TJbSSa8xyudYLc30KJvg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMorphometryStats
> However I did a saninty check and compared the  TGM_estimated=TGM_left + 
> TGM_right. with the measurement in the aseg file: Measure TotalGray, 
> TotalGrayVol, Total gray matter volume. They are similar but not the same.
> Which makes me wonder if this is not the proper ay of calculating it. 
> Therefore:
> which is the best way of calculating left hemisphere total grey matter volume 
> and right hemisphere total grey matter volume in a separated manner?
>
> Thanks in advance,
> Vicente Ferrer
> Predoctoral Researcher BCBL
> http://secure-web.cisco.com/1Y80FAmAIDLnW-nPDCMBRDUQbmyy9_KQJaimWnm60B6mbmpKCQ_tBro0XoY7GpznCvgE7QUEksgT-7X6bRkawyzmB7R54K979XH1_EU42r3LaC9vSzKV93hnwYreNA1GmBBYZqmbpO9-jjmltijKRbWEJIlAnf_VvlPquW9vBzNuHNzHj36jXiEi3vCzoWYO2jh5QNuppL1tJaUKtEQjf1kpzkhChnmujzSX_dd54PdS9SpwBSDeSgG7aYuqjrcFeBSHY2yaOll7yeKRIZXz6bA/http%3A%2F%2Fwww.bcbl.eu
>
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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Greve, Douglas N.,Ph.D.]

Can you send the full terminal output?

On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote:

External Email - Use Caution

I tried to run mri_vol2surf with the following command: mri_vol2surf --src 
/home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi 
lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i obtain an error 
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768. How can i fix it?

El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Which MNI space? If mni152, then run recon-all on the mni152 template, then run 
mri_vol2surf with --regheader  mni152subjectname; also include --projfrac 0.5. 
But before you do that , load the AAL atlas onto the mni152subject with the 
surfaces to make sure everything aligns. You might want to do this with the 
colin27 brain instead because I think that is what the AAL atlas is defined on.

On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:

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Hello everyone, I tried to follow your instruction about how to get the 
fresurfer stats in AAL ROIs. I have an image .nii with the labels of the AAL in 
the MNI space (i submit this image in the e-mail). Can I use this image in the 
mri_vol2surf? If so, i suppose that this image would be the input one, but i 
don't know what is registration file in the syntax of mri_vol2surf

Sorry for the inconvenience, Alberto



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Re: [Freesurfer] About mri_vol2surf {Disarmed}

[Greve, Douglas N.,Ph.D.]

tkmeditfv mni152 nu.mgz -surfs -seg aal.nii

On 11/18/2020 6:28 AM, Alberto Del Cerro Leon wrote:

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How can I load the AAL onto the mni152 subject with the surface?

El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:
Which MNI space? If mni152, then run recon-all on the mni152 template, then run 
mri_vol2surf with --regheader  mni152subjectname; also include --projfrac 0.5. 
But before you do that , load the AAL atlas onto the mni152subject with the 
surfaces to make sure everything aligns. You might want to do this with the 
colin27 brain instead because I think that is what the AAL atlas is defined on.

On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:

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Hello everyone, I tried to follow your instruction about how to get the 
fresurfer stats in AAL ROIs. I have an image .nii with the labels of the AAL in 
the MNI space (i submit this image in the e-mail). Can I use this image in the 
mri_vol2surf? If so, i suppose that this image would be the input one, but i 
don't know what is registration file in the syntax of mri_vol2surf

Sorry for the inconvenience, Alberto



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Re: [Freesurfer] mri_segstats question

[Greve, Douglas N.,Ph.D.]

I don't understand why WM was cropped out. What command were you trying 
to use?

On 11/18/2020 2:39 AM, RENXI LI wrote:
>  External Email - Use Caution
>
> Hi Freesurfer experts:
>
> I am trying to extract the mean-time series from the functional image using 
> mri_segstats. However, the cerebral white matter signals were cropped out in 
> my functional images, and the regions that I am trying to extract signal from 
> are close to the cerebral white matter that some voxels at the boundary may 
> not contain any signals. Is there any arguments in mri_segstats that I can 
> use to only extract voxels that has non-zero time-series?
>
> Best,
> Renxi
>
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Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

[Greve, Douglas N.,Ph.D.]

You mean that you are getting a different result between the voxel wise 
analysis and the ROI-wise analysis? And you created the ROI from the region 
that is significant in the voxel-wise analysis? If so, then I think something 
is wrong

On 11/17/2020 8:08 PM, 李梦君 wrote:

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I got the sum area and average area of the label, there is no significant 
difference between the mTBI group and health control, either.However, the label 
was significant different in the fsaverage between mTBI group and health 
control after multiple control. Did this correct?


-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-16 23:48:37 (星期一)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

The lh_areapial.avgwf.dat has a value for each subject. That value will be 
whatever the y.mgh is. If you want a different value, then create a new y.mgh 
file. Also, I forgot to tell you to include --sumwf so that the avgwf file has 
the sum and not the average.

On 11/14/2020 5:24 AM, 李梦君 wrote:

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  I am sorry for that my presentation was not that good, the lh_areapial.sum and

lh_areapial.avgwf.dat file are uploaded, I get only one area value in the 
lh_areapial.sum file

with the following command.

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0

My question was that how can I get the value of the area and volume in the 
standard space for every TBI and health control subjects.



-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-13 23:03:50 (星期五)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

sorry, I don't know what you are asking

On 11/12/2020 8:30 PM, 李梦君 wrote:

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Thanks! I get only one area value in the lh_areapial.sum file with this command:

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh lh.areapial.label
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0

(1)Should I extract the area and volume one by one with the following command 
for each subject:

mri_segstats
--i qdec/Areapial_15_L/y.mgh
--slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped 
to every subject from the fsaverage)
--avgwf lh_areapial.avgwf.dat
--accumulate
--sum lh_areapial.sum
--exclude 0


-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-12 22:23:13 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed}

No, the area will be under the "Mean" column. Sorry, I know it is confusing. 
Also, you will just want to use the 2nd row. You can eliminate the first row 
with --exclude 0


On 11/12/2020 5:39 AM, 李梦君 wrote:

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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after 
the mri_segstats command

(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?

(2) When I extract the volumes, the lh_volume.sum displays the unit for the 
volume is Area_mm2（Blue color). Is this correct?


ColHeaders  Index SegId NVertices Area_mm2  StructName  Mean  StdDev
  MinMax   Range
  1   0161058 81037.1   Seg   242940.32810.7312 
0. 3.8885 3.8885
  2   1  2784 1182.3Seg00013760.6619 0.2525 
0.7136 1.8140 1.1005

Following is the code for extracting volumes
mri_segstats
--i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.volume.label (This was the label extracted from the 
fsaverage after multi-correction)
--avgwf lh_volume.avgwf.dat (output file)
--accumulate
--sum lh_volume.sum (output file)



-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-11 23:58:20 (星期三)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed}

Sorry, try this

mri_segstats
--i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the 
fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
On 11/5/2020 10:26 PM, 李梦君 wrote:

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Re: [Freesurfer] qdec replacement

[Greve, Douglas N.,Ph.D.]

We don't have a GUI, if that is what you mean. The default now is to use the 
command line stream where you create your own FSGD file and contrast matricies, 
then run mri_glmfit and mri_glmfit-sim

On 11/17/2020 10:44 AM, Pagliaccio, David (NYSPI) wrote:
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Re: [Freesurfer] smoothing on ?h.w-g.pct.mgh files

[Greve, Douglas N.,Ph.D.]

Use mris_fwhm. Run with --help to get info. Make sure to use the --smooth-only 
option

On 11/17/2020 5:31 AM, Enrico Collantoni wrote:

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Dear Freesurfer experts,
I computed the gray to white matter signal intensity ratio using the pctsurfcon 
command and extracted the ?h.w-g.pct.mgh files. How can I conduct a smoothing 
procedure on these surface files?

Thanks for your help,


--
Enrico Collantoni
MD, Ph.D., Psychiatrist
University of Padua
Neuroscience Department



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Re: [Freesurfer] Cortical thickness volume ROI to surface {Disarmed}

[Greve, Douglas N.,Ph.D.]

Have you checked that the output of each of the stages is correct? Eg, does 
mydata_T1.nii.mgz overlay with MNI152 and with ROI_MNI? At the end of 
fslregister, there will be a tkregister command to visualize the regsitration. 
Do those look ok?

On 11/17/2020 4:48 AM, Alina Rojas wrote:

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Thank you for your response! Here the commands:


#register image to MNIspace
flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out 
mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat
#Create a registration from the ROI-anatomical volume to a freesurfer template 
subject
fslregister --s fsaverage --mov mydata_T1_MNI.nii.gz --reg tmp.dat
#Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface 
overlay.
mri_vol2surf --mov ROI_MNI.nii.gz --reg tmp.dat --projdist-max 0 1 0.1 --interp 
nearest --hemi lh --out lh.fsaverage.ROI_MNI.mgh —noreshape
tkmeditfv fsaverage lh inflated -overlay lh.fsaverage.M1_L.mgh -fthresh 0.5

I tried with another threshold, and to change it while in Freeview and it’s 
either the whole surface with the overlay or none.

Thank you for your help!

Alina Rojas




Am 16.11.2020 um 17:04 schrieb Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>:

please send the command line

On 11/16/2020 7:20 AM, Alina Rojas wrote:

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Hello Freesurfer experts,

I am attempting to register a ROI (.nii) to the surface of fsaverage to get the 
statistical output on the cortical thickness. I followed your instructions on 
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behttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
 but after mri_vol2surf I get this message, I can’t visualize the ROI on the 
surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, Alina 
Rojas.

srcvol = M1_L.nii.gz
srcreg = tmp.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
INFO: using NIfTI-1 qform
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between  COR types 
with c_(r,a,s) = 0.
Input reg is register.dat
 original matrix ---
 1.0   0.0   0.0   2.49380;
 0.0   0.0   1.0  -22.50500;
 0.0  -1.0   0.0  -9.53872;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface /fsaverage/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 1
using old
 2 0.1 0 1
using old
 3 0.2 0 1
using old
 4 0.3 0 1
using old
 5 0.4 0 1
using old
 6 0.5 0 1
using old
 7 0.6 0 1
using old
 8 0.7 0 1
using old
 9 0.8 0 1
using old
10 0.9 0 1
using old
Done mapping volume to surface
Number of source voxels hit = 75073
Writing to lh.fsaverage.M1_L.mgh
Dim: 163842 1 1
surfcolor: Subscript out of range.






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Re: [Freesurfer] question about PVC of PETSurfer

[Greve, Douglas N.,Ph.D.]

It is not set up to use the subfields. In principle it could be, but I don't 
think it would be very accurate because the subfields are so small.

On 11/17/2020 4:27 AM, 蒋袁芳 wrote:

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Hello Freesurfer,
We know that the freesurfer7 has given a new module to separate hippocampal 
subfields in MRI image, but we encoumter problems in registering the PET image 
with MRI image. We find that the resolution radio of PET image is not enough, 
it made the SUVr of hippocampal subfield we get is not accurate. So we want to 
use the PVC function of PETSurfer. Whether the PETsurfer output the result of 
PET image after PVC ? so that we can use it directly to registering with MRI 
image. If it doesn't output the result, can we save it in some ways? Thank you 
for your guidance.



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Re: [Freesurfer] use different parameters of MRI DICOM

[Greve, Douglas N.,Ph.D.]

What do you mean by one analysis? I don't think it would make sense to average 
the images together. If you mean that different subjects have different scans, 
then it is not ideal, but you could include scan as part of your statistical 
design. Just make sure that different populations are balanced across the 
different scans.

On 11/15/2020 9:47 PM, 王颖喆 wrote:

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Hello Freesurfer Developers,

I'm attempting to analyze data using freesurfer. The dataset we used includes 
two different series of MRI DICOM:
The first series (n=562) was collected using the following paremeters: t1_fl3d 
(Voxel Size = 0.9×0.9×1.5mm,  FOV = 220 mm, TR = 21ms, TE = 7.65ms, Flip Angle 
= 30⁰);
The second series  (n=300) : MPRAGE(Voxel Size = 1×1×1mm, FOV = 256mm, TR = 
2300ms, TE = 2.98ms, Flip Angle = 9⁰).
All brain MRIs were performed on the same 3.0T Siemens scanner.
I'd like to know if it is accpetable to include both of these imagings in one 
analysis? Is there any pre-processing step need to be done?
Thank you!

Yingzhe Wang








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