Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and send the file nucor.log
On 5/28/2021 7:51 AM, liub wrote:
External Email - Use Cauti
Try using tkregisterfv instead (it takes all the same command line args
but uses freeview
On 5/28/2021 2:13 AM, 张威 wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am attempting to manually register a cerebral blood flow images to a
T1 weighted images via the comm
There might be a couple things happening. First, I would try adding a
few control points in that area; make sure they are in true WM in voxels
that have a value less than 110 on the brain.mgz file. This might help
push the white surface further out (the WM in that gyrus is very thin).
It might
Can you check the registration of the FLAIR and T1?
cd subject/mri
tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta
--targ orig.mgz
On 5/20/2021 4:33 PM, Mark Wagshul wrote:
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Hi. I’m trying to run
You definitely do not want to use mni152.register.dat for this (I'm
surprised it even got close). Instead, register the orig.mgz to the
HCP842 template space, eg, with
mri_coreg --mov orig.mgz --targ HCP842.template.nii.gz --dof 12 --reg
reg.HCP842.lta
This will print out a tkregisterfv command
Try removing the trailing slash from the subject name, ie,
10100_S2654UFQ, not 10100_S2654UFQ/
On 5/26/2021 1:18 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi all,
I am trying to extract LGI measures as prescribed in *MailScanner has
detected a possible fraud attempt from "sec
you'll need to supply us with more information, eg, command lines and
why do you think it has the wrong dimensions
On 5/25/2021 11:53 PM, Mingyang Xia wrote:
External Email - Use Caution
Dear freesurfer expert:
My name is Mingyang. I want to preprocess fmri image and map the
timep
There is not one file for CSF or GM, but you can extract them from other
files. Eg,
mri_binarize --i aparc+aseg.mgz --ventricles --o ventricles.mgz
mri_binarize --i aparc+aseg.mgz --gm --o gm.mgz
You can use aparc+aseg.mgz as your brain mask
On 5/25/2021 6:14 PM, Camargo, Aldo wrote:
E
run it with -autorecon2 and -autorecon3
On 5/25/2021 1:47 PM, Camargo, Aldo wrote:
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Hi Bruce,
I was wondering if there is way to continue the process to recon-all
once I have done the recon-all with the option -autor
If the tkregisterfv command works without the --surf option, then just
use that
On 5/18/2021 12:04 PM, Gabor Perlaki wrote:
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Dear all,
I tried to check the talairach transformation under Freesurfer 7 linux
version (freesurfer-linux-centos6_x86_64-7.1.1-20
why I am asking.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, May 10, 2021 9:23 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats(
On 5/24/2021 12:32 PM, Francisca Ferreira wrote:
External Email - Use Caution
Dear Experts,
I am new to FS. I'm trying to run mri_glm fit
I've created FSGD with 2 classes -responders vs non-responders to a
given intervention- and 3 variables to be regressed out-according age,
gend
No, not really
fov is field of view = voxelsize*number of voxels
frames are the number of frames in the file (ie, the 4th dimension)
dof = degrees of freedom we never use
xyz-start - edge of the volume
voxel to ras transform converts a column-row-slice into a
right-anterior-superior coordinate in
Generally, control points are the way to go here. It looks like you have
put a bunch of them in cortex though
On 5/21/2021 12:14 PM, Kadwani, Manorama wrote:
Hi,
I am trying to correct the white matter segmentation in the second
image shown below. It doesn't include chunks of the temporal lob
If I understand you correctly, you have an ROI defined in the volume and
you want to transfer it to the surface. Is that right? First you should
look at the ROI in the volume along with the surfaces and make sure that
they pass through the ROI. I would generally use the projfrac-max option
for
I am looking at volume and fsaverage is(?) a
surface thing?
Haley
On Mon, May 10, 2021 at 11:15 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
It is saying that the mask
lhYeo2011_7NetworksConfidence_N1000.mgzdoes not have thee same
dimensions as the input. How
You could also run recon-all on the mni152 template, then run the
hippo/amyg seg on the output. It will give you the same bad segmentation:)
On 5/20/2021 9:21 AM, Iglesias Gonzalez, Juan E. wrote:
Hi Jessica,
There’s no direct way of doing this, since the atlas lives it its own
space and ther
This is more of a question for the PALM developer (whom I have cc'ed).
On 5/19/2021 8:15 AM, Marina Fernández wrote:
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Dear experts,
I used the function fspalm to run permutations with the following options:
fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm
The easiest thing to do is to create a new stats file that has the same
basic format as the aseg.stats but with your desired measures in them.
Then specify the new stats file with --stats=newstatsfile when you run
long_stats_slopes
On 5/19/2021 1:06 AM, AJ wrote:
External Email - Use
Just create a text file (not bfloat) where each row is a different time
point. You can have multiple columns and can specify how many of them to
use in the analysis.
On 5/18/2021 5:03 PM, Eli Bulger wrote:
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Hello,
I am working with task-based functional
Are you sure those are the dimensions? They do not look right. It should
be something more like ~12x1x1x120
Try running
mri_info --dim fmcpr.up.sm5.self.lh.nii.gz
On 5/18/2021 1:26 PM, Mingyang Xia wrote:
External Email - Use Caution
Dear freesurfer expert:
I am sorry to disturb
I'm not sure what is going wrong with it, but you can do this yourself with
mri_binarize --i aparc+aseg.mgz --match 7 --o bin7.mgz
Then do the same with 8, 46, 47
On 5/17/2021 6:39 PM, A.R. Sekar wrote:
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Hello exper
On 5/17/2021 10:16 AM, Ellen JOOS wrote:
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Dear Freesurfer team,
I am currently preparing my first fMRI study and used OptSeq2 for
creating the trial sequence. Since I am not experienced with the study
design in MRI (I mainly conducted EEG studies so far), I would
It is possible. Try running defect-seg to see where the defects are. Run
it with --help to get more info
On 5/13/2021 2:20 PM, Dierker, Donna wrote:
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Hi freesurfer experts,
I have some cases where sulci near the occipi
your tksurferfv command line is wrong
On 5/12/2021 6:06 AM, Bernardoni, Fabio wrote:
> External Email - Use Caution
>
> Dear Freesurfers
>
> I recently moved to FS7.1 and I was trying to reproduce my workflow I had
> with FS5.3.
>
> To visualize statistical maps, I had always used tksurf
This was fixed in 7.11. You can use that version or copy the attached
file to this location
$FREESURFER_HOME/matlab/freesurfer_read_surf.m
On 5/11/2021 2:28 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi,
I am using Matlab R2014a, and FS7.1.0
and receiving this error when I try
This is because it takes two passes through the transform. One takes
each target vertex and finds the closest source vertex. The other takes
each source vertex not already sampled and finds the closest target
vertex to make sure that every source is represented. With the 2nd step,
there may be
Can you run
mri_info /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz
On 5/10/2021 1:00 PM, Lara Foland-Ross wrote:
External Email - Use Caution
Hello,
I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple
chip with BigSur as the OSX.
To test out the insta
Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>> wrote:
Try
cd yoursubjectname/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
yoursubjectname
On 5/3/2021 4:31 PM, Caspar M. Schwiedr
refers to- for
future reference? When is it best to go through fsaverage?
Thank you for the information
BW,
Marianna
*Από:* freesurfer-boun...@nmr.mgh.harvard.edu
εκ μέρους του Douglas N.
Greve
*Στάλθηκε:* Δευτέρα, 10
did you draw the labels on each subject separately? In that case there
is no need to go through fsaverage.
Projfrac is the fractional distance between the white and pial surfaces
(0.5 is half way)
projdist is the absolute distance (eg, 1.5 is 1.5mm)
Generally projfrac is preferred as it adapts t
You should not need to. The files with the string .FSvoxelSpace in them
should already be in that space
On 5/10/2021 5:32 AM, Borghi, G. (Gregorio) wrote:
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Dear All,
Due to my study, I have been unsuccessfully trying to co-register the
hippocampal and am
lGI has a lot of native smoothness in it, often so much that it exceeds
the tables that we precompute. I would strongly suggest not using the
precomputed tables for this and instead use permutation. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 5/9/202
You should be able to use --target fsaverage5 (or fsaverage4)
On 5/9/2021 3:54 PM, Knut J Bjuland wrote:
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Dear Freesurfer experts,
Is it possible to run mri_preproc with ico with lower than 7, for
instance with ico e
ur help,
Andrew
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, April 25, 2021 10:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FA map registration to T1
Everything looks ok in the log file. Did you do an B0 distortion
corr
Can you be more specific that "weren't really good"?
On 5/6/2021 12:03 PM, Peled, Noam wrote:
Dear group,
I have preop and postop MRI scans of an epileptic patient.
I ran recon-all on the preop, and bbregister on the postop to register
it to the preop.
I’m not sure why, but the results wer
Try
cd yoursubjectname/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon yoursubjectname
On 5/3/2021 4:31 PM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi!
I am trying to make a ribbon.mgz from a
A better way to do this is to use mri_surf2volseg. Look in the
recon-all.cmd file for your subject and find the command that creates
the aparc+aseg.mgz file. Use that command but changing the annot file
and output file
On 5/6/2021 8:12 AM, Nakajima, Mitsuko wrote:
External Email - Us
It is trying to find a precomputed table of p-values based on the
criteria of your particular analysis. However, The smoothness of your
data is extreme, and the tables were not computed for such smooth data.
What is the nature of your data?
On 5/5/2021 11:29 AM, Paul, Rahul wrote:
Hi Freesurf
You can use use mri_binarize with --min 0.5 and it will take all labels
with value 1 and greater. You can create a bounding box with mri_mask
with the -bb option
On 5/4/2021 11:53 AM, Arman Avesta wrote:
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Hi gang,
I have downloaded head MRIs of 1000 subje
REgister the FDG to the anatomical (mri_coreg --s subject --mov fdg.nii
--reg fdg.reg.lta), sample the FDG into the anatomical space
(mri_vol2vol --mov fdg.nii --reg fdg.reg.lta --fstarg --o fdg.anat.mgz),
the use mri_segstats --seg
rh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz --i fdg.anat.m
Is there a reason that you are not using mri_glmfit-sim to do this? It
is fairly complicated, and so I spent a lot of time writing
mri_glmfit-sim to make sure it does the right thing.
On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:
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Dear Experts,
I am running
urface corresponds to what (x,y)
point on the flatmap.
Thanks a lot for your help.
Kind Regards,
Ornaith
On Tue, 16 Mar 2021 at 15:58, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:
your description is unclear to me
On 4/28/2021 12:23 PM, Mercy Mazurek wrote:
External Email - Use Caution
I loaded my brainmask.mgz file generated from a "recon-all
-autorecon1" command. When I open up Freeview, I see the icon but it
is grayed out and I cannot select it to create a
look in ?h.aparc.stats files
On 4/27/2021 2:17 PM, Nils B. wrote:
External Email - Use Caution
Dear Freesurfer developers,
I'm hoping you can help me once again.
Right now I'm working on how to extract certain measurements out of my
data set. I have two groups and MRI data from one t
table_desikan_killiany.txt)
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas
N. Greve mailto:dgr...@mgh.harvard.edu>>
*Sent:* Sunday, April 25, 2021 8:35 PM
*
Significant in group analysis of what? The commands look ok
On 4/27/2021 9:18 AM, LIN, Yezhe wrote:
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Dear Freesurfer experts,
My name is Yezhe Lin. I am trying to extract the thickness in an area
we found significant in group analysis. However, when we did
It is saying that the mask lhYeo2011_7NetworksConfidence_N1000.mgzdoes
not have thee same dimensions as the input. How was it created? It must
be a surface overlay on fsaverage
On 4/26/2021 6:59 PM, Haley Park wrote:
External Email - Use Caution
Hello,
I am trying to run a correlati
Yes, you can just average them
On 4/26/2021 3:59 AM, Agurne Sampedro Calvete wrote:
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Dear Freesurfer experts,
I am trying to obtain the average thickness of the brain lobes. I am
particularly interested in the temporal lobe.
I have run "mri_annotation2labe
It is not in the aseg. Look in the aparc+aseg and look for seg IDs 1035
and 2035
On 4/25/2021 3:54 PM, Kelli Ann Nini wrote:
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Greetings esteemed surfers,
I am trying to take an image of the insula using the LUT. I've l
What is your command line and terminal output?
On 4/24/2021 8:36 PM, Haneen Hakeem wrote:
External Email - Use Caution
*/Hello FreeSurfer Developers,/*
*/
/*
*/I’m attempting to output stat files using “asegstats2table” and
“aparcstats2table” but for some of my subjects I get the foll
On 4/24/2021 5:56 PM, AJ wrote:
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Hi,
Once SAMSEG has finished segmenting T2 lesions, other than trying
different --threshold flags, any way to manually modify them?
I'll let Stefano (cc'ed) weigh in.
Can --eTIV be added to SAMSEG?
Not sure what you mean
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, April 20, 2021 10:09 AM
*To:* freesurfer@nmr.mgh.harvard.edu
what is your mris_anatomical_stats command and terminal output?
On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:
External Email - Use Caution
Hello fellow Freesurfer users,
I am attempting to reproduce the analysis conducted by Parker et al.
in their 2018 paper, “Cortical microstr
Yes, exactly on both questions
On 4/22/2021 8:23 AM, Marilena Wilding wrote:
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Dear Freesurfers,
I’m currently doing 2nd level analysis on a FIR model.
I first concatenated my data with this command:
isxconcat-sess -sf
Yes, that looks good
On 4/20/2021 11:55 PM, Boa Sorte Silva, Narlon wrote:
External Email - Use Caution
Dear FS experts,
Hope this finds you well.
I would like to check whether the following the correct approach for
my models in glm_fit. I am testing whether gait speed is associated
Try adding a -p as below (-p indicates that it is a patch)
mris_convert -p lh.full.flat.patch.3d flat_lh.gii
On 4/20/2021 2:50 PM, Suzanne Nie wrote:
External Email - Use Caution
Hello Freesurfer Developers,
I'm attempting to create a full surfaces folder in the filestore based
on t
Can you send a few pics on what you are seeing?
On 4/20/2021 11:29 AM, Jindal, Saurabh wrote:
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Hi experts,
I am working on freesurfer 7.1 now and my ROI is hippocampus, but it
seems that there is some non-hippocampal i
It looks like you made some manual edits, then re-ran recon-all, but did
not do so fully (eg, used autorecon2 but not autorecon3). Does this make
sense?
On 4/20/2021 4:35 AM, 林鈺庭 wrote:
External Email - Use Caution
Dear FreeSurfer Developers:
We analyzed MRI T1 image data on freesur
and do they each have a norm.mgz?
On 4/19/2021 4:11 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Douglas,
I found the aseg.presurf.mgz for all cross sessions and base using
version 6.0.
Best,
Qi
On Sun, Apr 18, 2021 at 10:43 PM Douglas N. Greve
mailto:dgr
can you send the bbr log file?
On 4/19/2021 2:29 PM, Russo, Andrew William wrote:
Hello FreeSurfer Developers,
I am registering FA maps to T1 for a group of subjects with MS and in
many cases the registration is poor for the anterior corpus callosum
(attached), cerebellum, pons, and temporal
On 4/19/2021 1:07 PM, Jaime Gomez wrote:
External Email - Use Caution
Thank you Douglas for the answer. Could you be more explicit?
So, once you have the aseg.stats you need to run which command with --etiv-only?
On Mon, Apr 19, 2021 at 4:00 PM Douglas N. Greve
mailt
No, not yet. FLAIR itself would probably not be for this anyway as it
usually does not have good gray/white contrast
On 4/19/2021 10:00 AM, Jindal, Saurabh wrote:
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External Email - Use Caution
Hi experts,
Could we analyze FLAIR images using freesu
You should talk to them
On 4/19/2021 7:52 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
External Email - Use Caution
What is your advice for me now? Should I abandon the approach or is
there anyway to dig deeper into it and solve the error?
*From: *"Douglas N. Greve"
It is not done. If you are running asegstats2table, you can have it
perform the correction by adding --etiv to the command line
On 4/19/2021 7:41 AM, Jaime Gomez wrote:
External Email - Use Caution
Hi,
Does the asegs.stats produced by recon_all have the volume estimates
of subcorti
If you have the data in the native functional space, then just
mri_vol2surf --mov func.nii --hemi rh --reg reg.lta --trgsubject
fsaverage --projfrac 0.5 --o rh.func.fsa.mgz
On 4/19/2021 5:23 AM, Mason Wells wrote:
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Hi
?///
Thanks again for all your help.
Kindly,
Thomas Harkey
UAMS College of Medicine M3
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Wednesday, April 14, 2021 9:25 AM
*To
Check each of your cross time points to make sure that all have an
aseg.presurf.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:
h Centre PhD Student/
/Forensic & Neurodevelopmental Sciences/
/Institute of Psychiatry, Psychology & Neuroscience/
/King’s College London/
/16 De Crespigny Park, Camberwell/
/London, SE5 8AB/
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* 16 April
waiting
for that brainmask.mgz and cant find it. Has there been any
collaboration between freesurfer and fmriprep people on this matter?
Thanks
Shervin
*From: *"Douglas N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Friday, April 16, 2021 at 11:08 AM
*To: *&
Copy the lta to subject/mri/transforms/FLAIRraw.lta (there should be one
there already, just copy over it)
On 4/16/2021 12:19 PM, Edina Szabó wrote:
> External Email - Use Caution > > Hi Douglas, > > Thank you for your
response! I really appreciate it. > > I ran the command – it works if I
r
Not sure what is going wrong here. Try running
mri_annotation2label --subject myatlas.i3 --hemi lh --outdir
/media/chenlz/Zixuans1/MRI_Data/Human_MRI/CCS_PrePro/myatlas.i3/make_cortex_label.tmp.8214
--annotation aparc.a2009s
Does it segfault in the same way?
Can you confirm that you are not run
Yes, this is a known error that will be fixed in 7.2, thanks for
pointing it out
On 4/9/2021 2:51 AM, Yoonho Hwang wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compute cortical thickness and to analyze it between
groups.
So I perform "recon-all"
ensic & Neurodevelopmental Sciences/
/Institute of Psychiatry, Psychology & Neuroscience/
/King’s College London/
/16 De Crespigny Park, Camberwell/
/London, SE5 8AB/
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* 15 April 2021 15:14
*To:* freesurfer@nmr.mg
, here is the copy of recon-all.log
*From: *"Douglas N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Wednesday, April 14, 2021 at 10:32 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Autorecon1 failure
Sorry, can you resend the recon-all.log file?
It looks like you have only a single 64 sec polar/eccen cycle to your
acquisition. Is that right? It is pretty slow.
On 4/16/2021 9:44 AM, Michaël Vanhoyland wrote:
External Email - Use Caution
Dear Freesurfer team,
I'm new to fMRI analysis and want to analyse Retinotopy data. I was
You can just run recon-all -s subject -qcache
this will only run the qcache
On 4/16/2021 1:57 AM, Vishnu S wrote:
External Email - Use Caution
Hello,
I downloaded some FreeSurfer recon-all analyses from the ADNI dataset,
but these analyses have been run without the qcache flag.
Is t
Y07fNKPRzLLPjnnMcUvYxT3W6DxKSKqeDT2JSB9imewWGcOu7selP30CVzIeH_jhhiwWpMCVUex9xfzB01IgEo6strRSHUl6inLA_0n62Mw/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%2540nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2Bmri_gtmpvc%2Berror%255C%253A%2Bfailed%2Btissue%2Btype%2B
The input is a table, so the output is a table (the sig.mgh file will
just have the number of values that are in the table; this is not a
"volume" you can look at in FV). Look in the sig.table.dat file for the
sigs.
On 4/13/2021 8:41 AM, Griem, Julia wrote:
External Email - Use Cauti
Try adding --empty
On 4/12/2021 4:58 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Experts,
I am using mri_segstats with the --ctab flag to extract dti and suvr
values from a white matter hyperintensities parcellation. Running
mri_segstats on the image and parcellati
Thanks, I just fixed it and pushed the change. Should be in the next
version.
On 4/12/2021 3:05 PM, Ben Singer wrote:
> External Email - Use Caution
>
> On line 106:
>
> if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then
>
> there should be a "$" before the "UseOctave" to make the line re
What are the voxel sizes in the native space? It may be that if it were
shifted one voxel over, it would be shifted too far in the other direction.
On 4/12/2021 10:42 AM, Larson, Kathleen E wrote:
External Email - Use Caution
External Email - Use Caution
Hi again,
I realized
This means that the source or target of the registration is not the same
as what is in the registration file. Did the subject folder change? You
can always delete the registration and rerun, and it will register to
the new target
On 4/9/2021 10:58 AM, Manenti, Giorgio wrote:
> External
Can you send the log file of the run using the nifti as input? The file
you attached is for dicom input.
On 4/8/2021 8:39 AM, Banu Femir wrote:
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Dear FreeSurfer Developers,
I've a problem that cannot solve for the last week. I am using virtual
box, FS7 o
Yes, I think you should be able to do that. It would be something like
mris_apply_reg --sval rh.thickness --tval rh-on-lh.thickness.mgz --streg
xhemi/surf/lh.fsaverage_sym surf/lh.fsaverage_sym
On 4/7/2021 4:55 PM, Ghassemieh, A. (Anna) wrote:
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Dear all,
It looks like you are running a T2 through recon-all, which won't work.
recon-all only takes T1-weighted. You can run it through samseg, eg,
samseg --i T2_age_reg_bias.nii.gz --o samseg
You can then binarize the seg.mgz to get everything inside the skull
On 4/7/2021 2:17 PM, Rohan Bareja wrote:
Sorry, can you resend the recon-all.log file?
On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
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*From: *"Abdollahi, Shervin (NIH/NINDS) [C]"
*Date: *Thursday, March 18, 2021 at 12:42 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Autore
For the aseg.stats, you can run mri_segstats. Look in recon-all.cmd for
the command that creates the aseg.stats file and change the input and output
On 4/7/2021 8:24 AM, Marques Ana-raquel wrote:
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Dear Freesurfer Team,
We would like to perform a striatal
Sorry, there is not a good way in v7
On 4/7/2021 2:57 AM, Marion DURTESTE wrote:
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Hi Douglas,
Thank you very much for your answer!
What would you suggest is therefore the best way to do this in V7?
Best wishes,
Marion D
Le 2021-04-06 15:18, Douglas N
2020 uninstall.sh
On Apr 6, 2021, at 22:30, Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>> wrote:
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
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Hi,
I am trying to m
:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, March 25, 2021 9:48 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1
That is an axial scan that only covers 25mm of the brain
inferior-superior. This is not
reeview.app and loading a volume with it./
On Mon, Apr 5, 2021 at 6:43 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
It looks like you are still using the old make_average_subject as
the time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can
you confirm that
If it is just visualization, you should be able to just load them in
Freeview (assuming that they share the RAS system)
On 4/6/2021 3:01 PM, Fischl, Bruce wrote:
Hi Noam
You can always use the -rl switch in mri_convert (rl ==
“reslice like”). So for example
mri_convert -rl rawavg.mgz ori
It is expecting a voxel shift map, which won't work with topup. One
thing you can do is to do the preprocessing (motion correction, slice
timing correction, topup) outside of fsfast, save the output as
something like f.mypreproc.nii.gz, then specify -funcstem f.mypreproc
when running mkanalysis
hing specific I need to check?
Thanks in advance,
Kind regards
On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
You will need to create a new color table. This is not hard, but
not easy either. First, there should be a color table already
Anything with 0 thickness is assumed to not be a valid cortical vertex.
As such, we don't smooth it so that it does not corrupt other vertices
that are valid. When you stack the images together and use this masked
smoothing, any invalid vertex will become 0 for all subjects and will be
ignored
Twice the same image at 1x1x1, then use mri_robust_template to register
and average them together
On 4/6/2021 8:10 AM, Ramesh Babu wrote:
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Dear Eugenio and Philipp,
Thank you very much for your suggestions. Could you please give more
input on "acquire the
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
> External Email - Use Caution
>
> Hi,
> I am trying to make an average subject but when the process reaches
> mris_average_surface it fails as seen below.
> My comm
why do you need to connect to the web site? that is not needed to run FS
On 4/5/2021 3:20 PM, Swearingen, Hannah wrote:
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Hi,
I am setting up an Access Control List for an isolated VLAN in which
my center's neuroimaging computing workstations will be connec
--in-intensity-units MR --subject 218
--surf-wm-vol --etiv/
El lun, 5 abr 2021 a las 15:50, Douglas N. Greve
(mailto:dgr...@mgh.harvard.edu>>) escribió:
What are your command lines?
On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:
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