alf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, November 18, 2020 6:09 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] -openmp vs -threads,
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
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:
Yes, that is correct
On 11/19/2020 11:43 AM, Batool Rizvi wrote:
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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
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:
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Hi Bruce,
Thanks for the prompt reply. It is my understanding that
Can you upgrade to 6 or higher?
On 11/13/2020 1:32 PM, Wei Shao wrote:
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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
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:
External Email - Use Caution
Dear experts!
I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I
would like to convert
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
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
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
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
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
tkmeditfv mni152 nu.mgz -surfs -seg aal.nii
On 11/18/2020 6:28 AM, Alberto Del Cerro Leon wrote:
External Email - Use Caution
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>>)
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
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:
External Email -
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:
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:
External Email - Use Caution
Dear Freesurfer experts,
I computed the gray to white matter signal intensity ratio using the pctsurfcon
command and
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:
External Email - Use Caution
Hello Freesurfer,
We know that the freesurfer7 has given a new module to
Just use --meas volume instead of --meas area
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Sara Lyn
Sent: Thursday, November 19, 2020 12:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Group Analysis {Disarmed}
External Email
Sorry, meant to say instead of --meas thickness
From: Greve, Douglas N.,Ph.D.
Sent: Thursday, November 19, 2020 1:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Group Analysis {Disarmed}
Just use --meas volume instead of --meas area
They are exactly the same. The two flags go to the same code.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of d m
Sent: Wednesday, November 18, 2020 5:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] -openmp vs -threads, -parallel
No, you are not overwriting anything.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of gunes
Sent: Monday, October 5, 2020 12:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Parallel Run of Multiple Patients
External Email - Use
In principle you can, but it might require a lot of work. You can use something
like
mri_binarize --i aparc+aseg.mgz --replaceonly X Y --replaceonly X2 Y ...
where X is the seg no for a given cortical segmentation and Y is the seg no for
the lobe it belongs to. You would do this for all
Do you mean you want a binary mask of the medial wall?
You can create a mask of the cortical label (?h.cortex.label) with
mri_label2label
You can then invert that with something like
fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz
On 1/28/2020 6:31 PM, Alexopoulos, Dimitrios wrote:
run anything, just check options and exit
--help print out information on how to use this program
--version print out version and exit
Thanks,
On Mon, Jan 27, 2020 at 6:03 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Run it with --help. Also look at the PETsu
the label I created to you in attachment.
Please, let me know if you have any problem with it.
Thank you.
On Sat, Jan 25, 2020 at 12:24 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
I'm guessing that there is something wrong with the label. Can you send it?
On 1/21/2020 8:08 PM
rfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 16, 2020 3:40 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [
Have you looked at your images to confirm that there is nothing really wrong?
Look at orig.mgz, brain.mgz, and aseg.auto_noCCseg.mgz
On 1/21/2020 11:02 AM, Desel, Tenzin wrote:
Hello FreeSurfer Developers,
I'm attempting to run recon-all after unpacking data. It is exiting with errors
-
I think that is going to be tough. Maybe you can edit the wm.mgz so that the
orig surface starts in the right place. I don't think control points are going
to work very well
On 1/21/2020 10:31 AM, Jane Tseng wrote:
External Email - Use Caution
Dear Freesurfer experts,
I would like to
er command using the flag
--bonferroni 2. Could you please confirm is that's the correct way?
Not sure. You can just multiply the p-values that you get out of PALM by 2
Thanks.
On Fri, Jan 10, 2020 at 10:43 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
sorry, I'm not sure I
Run it with --help. Also look at the PETsurfer wiki page for typical usage
On 1/27/2020 3:54 PM, Kate Marvel wrote:
External Email - Use Caution
Hi Freesurfer community,
I would like to know the arguments to use for symmetric Geometric Transfer
Matrix and two-compartment model
correct
On 1/24/20 10:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Ok. But the updated patches will need to be applied to the data generated with
the -hires flag?
Jim
On Jan 24, 2020 5:32 PM, "Greve, Douglas N.,Ph.D."
<mailto:dgr...@mgh.harva
if there is any habituation between runs of our task. Is there a way
to concatenate each run separately?
Message: 15
Date: Fri, 24 Jan 2020 15:36:36 +
From: "Greve, Douglas N.,Ph.D."
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] help: fs-fast group level
For the -conf2hires, there is no problem because the segmentation is done at
1mm.
On 1/24/2020 5:17 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I came across info for version 6.0 that generated statistical errors when using
high resolution input.
The run-wise functionality was added after selxavg was written as a way to help
debug. If you want all the runs in your group analysis, why not turn off the
run-wise flag?
On 1/22/2020 4:40 PM, Rami Hamati wrote:
External Email - Use Caution
Hello freesurfers,
I'm attempting to run
It did not look like there was an explicit error in that log file, it just
stops at mris_volmask. Is that the right recon-all? Also, please just send the
text file so that we don't have to unzip it.
On 1/22/2020 4:39 PM, Laurel Quinlan wrote:
External Email - Use Caution
Hi FS
On 1/22/2020 2:13 PM, Graduate Imaging wrote:
External Email - Use Caution
On Tue, Jan 21, 2020 at 10:40 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
On 1/17/2020 10:39 AM, Graduate Imaging wrote:
External Email - Use Caution
Hello,
I recent
you will have to create a binary mask from the sig map by thresholding at a
given level, eg,
mri_binarize --i sig.mgh --min 2 --o sig.bin2.mgh
Then run
mri_segstats --i y.mgh --seg sig.bin2.mgh --id 1 --avgwf y.bin2.dat
where y.mgh is the --y input to mri_glmfit
--id 1 means to take the
On 1/22/2020 2:54 AM, Christian Krog Tamnes wrote:
External Email - Use Caution
Dear FS experts,
I came across this post about a bug related to global measures of volume from
version 6.0:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed
I have two questions that I hope
I would normalize all the variables. Eg, column 2 is nearly identical to column
1
On 1/22/2020 1:03 AM, vittal korann wrote:
External Email - Use Caution
Dear Douglas
I did normalize ICV values. This is something else I guess.
With regards
Vittal
On Tue, Jan 21, 2020 at 6:09 PM
This error was still showing like it never end until I close freeview.
I draw the ROI in qdec, then add selection to ROI , and save the current
label. That was how I created the label.
I am looking forward to hearing from you. Thank you.
On Wed, Jan 22, 2020 at 12:17 AM Greve, Douglas N.,Ph.D
. Could it be
the reason?
Em ter, 21 de jan de 2020 12:29, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> escreveu:
Which version of FS are you using? I don't have this problem in v6 or dev. What
OS are you using?
On 1/17/2020 9:09 AM, Marcos Martins da Silva wrote:
External
-- Forwarded message --
Date: Thu, 23 Jan 2020 03:37:12 +
From: "Pizzagalli, Diego A.,Ph.D."
To: 'Help Desk -- Sam Mehl'
Subject: RE: FW: Post-doctoral Positions in Affective Neuroscience at McLean
Hospital/Harvard Medical School
I'd be very grateful if you could forward
sholded overlay.
>
> Thank you so much for the attention!
> Best,
> Pedro
>
>
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> On Behalf Of Greve, Douglas N.,Ph.D.
> Sent: Friday, January 10, 2020 11:12 AM
> To: freesurfer@nmr.mgh.harvar
You can only specify one input dicom file. We have a tutorial on how to
find that one file in a subject. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice
On 1/21/20 3:58 PM, Benjamin Ineichen wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I try
Try normalizing your covariates (ie, remove the mean and divide by the stddev)
On 1/21/2020 7:39 AM, vittal korann wrote:
External Email - Use Caution
Dear FreeSurfer experts
I ran QDEC and got the following error.
Design matrix --
1.0 1.04000 -1.38574
Don't smooth them! Smoothing creates partial volume effects. When you convert
to nifti, you have to be careful to make sure that any DICOM intensity scaling
is taken into effect; it is becoming more common these days. The only other
thing may be to remove the gradient distortion from the MRI if
On 1/17/2020 10:39 AM, Graduate Imaging wrote:
External Email - Use Caution
Hello,
I recently ran a vertex wise analysis on two different projects the first had
three groups with three co-variates that looked at if group membership was
associated with brain volume. The second
from clusters, but not the thickness from each subject at vtmax. And
I know if the input boxes were working I could get the scatter plot from vtmax,
so I guess there is a function inside both Qdec and TkSurfer to return this
information.
Em qui, 16 de jan de 2020 20:36, Greve, Douglas N.,Ph.D
; am not really sure whether the rule that the ID must not be in the files
> makes any sense at all. Maybe I can get around this.
>
>
> Best,
>
> Tim
>
>
>
>
>> On January 17, 2020 at 12:23 AM "Greve, Douglas N.,Ph.D."
>> wrote:
>>
>&
to debug
MRISalloc(15124178, 76): could not allocate faces
Cannot allocate memory
What do you mean how many point? How do I find it?
On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Is the label valid? Can you load it on a surface? How many
pen?id=1vkSRHeTPEn-UE4iighsStYbNkrzn03PG>
- paradigm files for expanding ring and for rotating wedge
Thank you for your precious help,
Marco
On Fri, 3 Jan 2020 at 17:51, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Can you send your paradigm files? Can you also send
PEn-UE4iighsStYbNkrzn03PG>
- paradigm files for expanding ring and for rotating wedge
Thank you for your precious help,
Marco
On Fri, 3 Jan 2020 at 17:51, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Can you send your paradigm files? Can you also send the terminal output? One
more th
toyama-no-iMac.local
machine x86_64
user toyama
UseRobust 0
Constructing seg from label
Segmentation fault
Could you help me please?
On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry, it should have been --sum instead of --o
the subjec
, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,
mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1
--o sum.dat
The mean value will be in the "Mean" column of the sum.dat
On 1/14/2020 7:08 PM,
please provide me more details?
Do you have any other suggestions?
Thanks again for your help
Dave
Il giorno sab 11 gen 2020 alle ore 15:56 Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> ha scritto:
YOu can try running mris_remove_intersection (or something like that)
On 1/11/2020
It is seg faulting at the defect correction stage which is before the FLAIR
would be used. At this point it should be identical to the T1-only analysis.
Check your commands to make sure they are the same except for the FLAIR part
On 1/16/2020 9:55 AM, Swanson,Clayton wrote:
External
On 1/15/2020 3:08 PM, Graduate Imaging wrote:
External Email - Use Caution
Hello,
I recently ran a vertex wise analysis on two different projects the first had
three groups with three co-variates that looked at if group membership was
associated with brain volume. The second project
I don't think so, but you can run mris_ca_label by hand. Look in the
recon-all.log file for the command, then use the 2005 tif instead of the 2009
tif. I think it should work.
On 1/16/2020 3:31 PM, Grodin, Erica wrote:
External Email - Use Caution
Hello,
I am running recon-all on my
Sorry, qdec and tksurfer are becoming (have become?) obsolete. I think you can
load an fsgd file in freeview
On 1/15/2020 11:02 AM, Marcos Martins da Silva wrote:
External Email - Use Caution
Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with
input/entry/edit
Nothing wrong per se, it is just that the inflation was done assuming a certain
number of vertices. You can try changing the number of iterations in the
inflation with,eg,
cd $SUBJECTS/fsaverage/surf
mris_inflate -dist .01 -f .001 -no-save-sulc 5 lh.smoothwm lh.inflated
In this case I set it to
It might be easier to use mri_segstats, eg,
mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1
--o sum.dat
The mean value will be in the "Mean" column of the sum.dat
On 1/14/2020 7:08 PM, Tien Pham wrote:
External Email - Use Caution
Dear FreeSurfer
Sorry, what is "pc1"?
On 1/14/2020 9:44 AM, Swati Rane wrote:
External Email - Use Caution
Hello,
I was wondering if someone could answer my question below
Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files.
Are there any set of parameters that should be set
Hi Tim, can you send a list of files that have the identifier. For
volumes and surfaces, it might be as easy as running
mri_convert/mris_convert using the same file as input and output.
On 1/13/2020 5:54 AM, Tim Schäfer wrote:
> External Email - Use Caution
>
> Dear FreeSurfer experts,
1.623 0.1824
129 2034 ctx-rh-transversetemporal cortex 210 25.529
1.678 0.0695
130 2035 ctx-rh-insula cortex 1499 383.186
1.295 0.0828
Am 10.01.2020 um 18:45 schrieb Greve, Douglas N.,Ph.D.
mailto:dgr
to perform the eddy current reduction?
Thanks a lot
Regards
Adam
Od:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
za uživatele Greve, Douglas N.,Ph.D.
YOu can try running mris_remove_intersection (or something like that)
On 1/11/2020 12:48 PM, Davide Momi wrote:
External Email - Use Caution
Dear Freesurfer expert,
I am working with bem model and I have created the outer and the inner skull.
Unfortunately, for few subjects the two
We don't have anything to denoise. You can try using ANTS DenoiseImage, but
using on the input might change where the surface is placed. We are
experimenting with using it inside the stream in a place where it is less
likely to bias the surface placement.
I don't understand the eddy current
+BN_Atlas_subcotex.mgz --atlas
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca'
--o BN_apas+head.mgz
Any ideas on that?
Best,
Boris
Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:
Are you sure you have permission t
I think this was answered yesterday. Check the previous posts
On 1/9/2020 7:58 AM, Kirill Elin wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
I am trying to run the script and the recon-all command and getting
Exited with errors output.
1. FreeSurfer Version
That in and of itself is probably not problematic as it is in the medial wall.
But I'm a little worried that the subcortical segmentation is not accurate. Can
I take a look at the subject? You can get it to me with:
>From the linux command line,
Create the file you want to upload, eg,
cd
I think you can just give each trial a different condition number in
the paradigm file
On 1/8/2020 3:04 PM, Katsumi, Yuta wrote:
> Dear Doug,
>
> I would like to perform GLM on a trial-by-trial basis in FSFAST. That is, I'm
> interested in obtaining beta estimates per trial and using them as
Yes, that is a valid solution. Thanks for giving us a heads up.
doug
On 1/8/2020 2:43 PM, Lewis, Lydia R. wrote:
Hello Freesurfer Team,
I am running the fsfast analysis stream for resting state data and recently
came across an issue with the funcroi-sess command. I originally used
sorry, I'm not sure I'm following. It looks like you did two analyses, one with
10mm smoothing and CFT=.05, the other with 12mm and CFT=.001. You get a cluster
for each in the same area, but they are not overlapping. Is that right?
On 1/6/2020 2:58 PM, Martin Juneja wrote:
External
Did you check the registration to see if it is ok? If it is ok (or if you fix
it), you can then turn off the talairach check with -no-tal-check
On 1/9/2020 4:32 PM, Isabella Leung wrote:
External Email - Use Caution
Hello Freesurfer Community,
I have been processing my T1 data through
when you make the average subject, just use --ico 5
On 1/9/2020 11:15 AM, Marina Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
Now, I would like to downsample the average subject of a dataset (that is a 7th
order icosahedron tesselation) to have surfaces with
On 1/9/2020 10:23 AM, Steve Petersen wrote:
External Email - Use Caution
Dear Freesurfer experts,
I would like to perform external analysis with the hippocampus, parahipocampus
and entorhinal volume. As I understand its the hipocampo volume should be
corrected using the subject´s
Your FSGD and command look correct. As for whether it is a good idea or not,
I'm not sure (you're probably the best person to decide that). One thing to
keep in mind is that if there are true thickness differences you might see some
differences due to partial voluming. I would also remove the
If you don't care about the affect hemisphere, I think you can just specify to
analyze only the unaffected with --hemi lh or --hemi rh
On 1/10/2020 8:19 AM, Horn, Mitchell Jacob wrote:
Hi Freesurfer Team,
I have a couple cases with large hemispheric ICH that have caused my recon to
hit the
I also usually use spm intensity noramlization, but I think you could
also use fsl.
On 1/6/2020 11:45 PM, falk.luesebr...@med.ovgu.de wrote:
> External Email - Use Caution
>
> Dear Manoj,
>
>
> in case you want to rely on tools provided with FreeSurfer only, N3 can
> produce good
pecify any projection fraction in our mri_vol2surf. Sorry for not
> being clearer in the step of analyze measured signal. We aim to make a brain
> mask of such hypointense signal and obtain its proportional area to total
> brain pial surface.
>
> Thank you so much for the attention Dr. Grev
No, sorry
On 1/6/2020 6:54 PM, Emilie Reas wrote:
External Email - Use Caution
I am running mri_glmfit using the --pvr option and do not get a pcc.mgh file
with the output. I found an old thread from 2017 in which Douglas Greve
explained that "mri_glmfit will not generate a pcc file
I think that should work, but I have not used the "ico" subject in a
long time. It would be safer to use --trgsubject fsaverage. But you can
also verify that they give the samme thing
On 1/8/20 12:12 PM, Marina Fernández wrote:
>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thanks
Not directly as an external regressor. You would have to extract the
info and create a waveform, one value for each TR in the external
regressor file. You might also want to convolve it with a hemodynamic
response function
On 1/8/20 11:15 AM, Swetara Joshi wrote:
>
> External Email -
Use --trgsubject fsaverage5 (you might have to link it to your
SUBJECTS_DIR). Also, how did you compute the register.dat? If you've
normalized it to MNI152, that will complicate things. Was the
normalization linear and nonlinear?
On 1/8/20 8:03 AM, Marina Fernández wrote:
>
> External
Are you sure you have permission to view that file?
On 1/6/20 5:01 PM, Boris Rauchmann wrote:
> External Email - Use Caution
>
> I’m sure just double checked it. I don’t know what’s wrong here.
>
> Von meinem iPhone gesendet
>
>>> Am 06.01.2020 um 18:35 sch
egmentation from
> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
> ERROR: cannot find aseg
> MacBook-Pro:mri boris$
>
>
>> Am 03
Hi Pedro, what you are trying to do is certainly possible. It looks like
you are doing the right thing as far as I can tell, but I got a little
lost after step 4, particularly the "Analyze measured signal" step. One
other thing that may be an issue is what projection fraction you used in
the
would really appreciate your help in fixing these errors.
>
> Thanks,
> Sahil
>
> On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Can you send the recon-all.log file? You sent the .error file
>
> On 12/20/
I don't think that will make a difference
On 12/20/2019 3:17 PM, Dincer, Aylin wrote:
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Hi FreeSurfer Experts,
Would upgrading computer hardware affect FreeSurfer output? We are using
FreeSurfer version 5.3-HCP and we are considering upgrading our server.
Can you send your paradigm files? Can you also send the terminal output? One
more thing, can you send the X.mat file from the output folder?
On 1/2/2020 3:19 AM, Marco Ninghetto wrote:
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Hello experts,
I'm performing retinotopy analysis but when running the
, 149-2615
Charlestown, MA, USA, 02129
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Se
e file BN_Atlas_subcotex.mgz was created using:
mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
$SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
Best,
Boris
On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harva
General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
From: Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 1:18 PM
To: Nasiriavanaki, Zahra
<mailto:znasiriavan...@mgh.harvard.edu>;
rch Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
____
From: Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 11:46 AM
To: Nasi
Probably not. The main diff between the current dev and stable 6 is that stable
6 had some big triangles near the top of the head
On 1/2/2020 11:39 AM, Dorian P. wrote:
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Are the fsaverage versions coming from the following (as reported in
recon-all.log
You can probably get a list of the changes from github, but there is no way to
separate out which ones are major and which ones are minor.
On 1/2/2020 11:36 AM, Dorian P. wrote:
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Hello everyone, and happy new year.
I know it's never a good idea to mix
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 10:57
look at the mgz file with freeview and it actually looks fine to me.
Its the subcortical segmentation of the BN atlas.
Do you have any ideas what went wrong?
Best,
Boris
On Tue, Dec 17, 2019 at 6:33 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
OK, I'm still at a loss
Can you send the recon-all.log file? You sent the .error file
On 12/20/2019 10:13 AM, Sahil Bajaj wrote:
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Hello FS experts,
I am trying to run recon all on about 100 subjects. But one out of 100 subjects
finishes recon all with error, and doesn't complete
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