Can you verify that that run has the proper number of frames (eg, it
does not have a single frame)? Did it create fmcpr.mcdat and/or
mcdat2extreg.log? In the projectdir/log folder, there should be a file
with a name like /mc-subjectname-bold.log. Can you send that?
On 4/10/19 4:30 PM, Mcnorgan,
That will compute the average of the Age slope and the NHPT slope.
Probably not what you want to do
On 4/6/19 12:24 PM, TMS lab wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer team,
>
> I'm running a correlation analysis where I'd like to corelate
> myelination and a clinical
Have you looked at the images to verify that there are no major problems
with it? Can you run it outside of the HCP pipeline to make sure it is
not an interaction?
On 4/8/19 12:52 PM, Jayasekera, Dinal wrote:
>
> External Email - Use Caution
>
> Dear all,
>
>
> I have been running versio
check out
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 4/11/19 10:58 AM, Abby tang wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers, I'm attempting to recon-all subjects but
> for some of my subjects I get the following error w
at I should be doing differently?
>
> Thanks,
> Katie
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D.
> [dgr...@mgh.harvard.edu]
> Sent: Monday, April
with the following matrix:
> 0 0 1
> And it seems to work. Is it ok this matrix?
>
> Thanks a lot
> Rafael
>
> Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> That will compute the average of the Age
Hi Amrita, first of all, thanks for following the instructions on
submitting the bug report! It helps us a lot to get all the information
the first time. As for your issue, there is a confound between the
Female class and the NSI_1 variable. All the Females have a NSI_1 value
of 0, meaning that
DOSS format since it won’t be ok for my
> other 6 variables. I would appreciate it if you could guide me through it.
>
> Best
> Amrita
>
> On Thursday, April 11, 2019, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Hi Amrita, fir
Well, you could go through and correct them, then count the number of
corrections:). But I don't think there is an automated procedure. You
could count the number of topological defects (but these are fixed
anyway). The values are in the aseg.stats file
On 4/11/19 3:38 PM, Weber, Wade A wrote:
are right. I want simply to correlate myelin and nhpt regressing
> > out age.
> > I did it with the following matrix:
> > 0 0 1
> > And it seems to work. Is it ok this matrix?
> >
> > Thanks a lot
> > Rafael
> >
> > Il giorno gio 11
The value of what is too high?
On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
>
> Hi
>
>
> I have not got the answer to my question yet, and I appreciate if you
> could please let me know what you think about it.
>
>
> Thanks
>
> Mona
>
> ---
t;
> mri_segstats --i
> $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg
> $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.har
try
recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3
On 4/11/2019 10:01 PM, Romella Durrani wrote:
External Email - Use Caution
Hello,
I am having problems generating the aparc stats files for all my scans. I have
checked the surfaces for all scans and they were all
/surf/lh.orig.nofix:visible=0
Hope you can give me more advises. Thank you very much.
Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>
于2019年4月11日周四 下午11:23写道：
check out
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 4/11/19 10:58 AM, Abby tang wrote:
>
>
Try
mri_binarize --i seg.nii --replaceonly segno1 segno2 --o newseg.nii
which will merge segno1 into segno2
On 4/12/2019 6:54 AM, Vidal Maxime wrote:
> External Email - Use Caution
>
> Hello,
>
> I have a t1w.nii file and a segmentation.nii file. For the latter, I was
> wondering how I c
You'll need to either convert the time series data into the conformed space or
the segmentation into the functional space. The first is probably better (it
will create a huge file but you can delete it when you are done). Use
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o
f
can say that the
-- Forwarded message --
From: Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>
Date: Thursday, April 11, 2019
Subject: Fw: mriglmfit error
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.
Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz?
Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or
fmcpr.odd.sm6.mni305.2mm.nii.gz?
Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D."
<mailto:dgr...@mgh.harvard.edu> ha scritto:
You
It looks like you are trying to do a surface-based analysis using a mask
derived from the volume-based fmri analysis. Is that right? And the fMRI is on
the mni152? If so, then you will need to get your mask onto the surface of
fsaverage. The easiest way to do that is to run recon-all on the mni
It looks like you are trying to do a surface-based analysis using a mask
derived from the volume-based fmri analysis. Is that right? And the fMRI is on
the mni152? If so, then you will need to get your mask onto the surface of
fsaverage. The easiest way to do that is to run recon-all on the mni
Use bbregister to create the register.dat file. Run it with --help to
get docs on how to use it.
On 4/15/2019 7:51 AM, Juhyoung Ryu wrote:
> External Email - Use Caution
>
> Hi all,
>
> I’d like to upsampling anatomical ROI data, what i created using ribbon file,
> to the functional res
want alignment between anatomical and functional data.
>
> Could you please tell me more about your suggestion?
>
> Thank you very much in advance!
> Juhyoung
>
>> On 15 Apr 2019, at 11:42 PM, Greve, Douglas N.,Ph.D.
>> wrote:
>>
>> Use bbregister to creat
in advance!
> Carolin
>
>
> Screen Shot 2019-04-12 at 5.29.44 PM.png
> Screen Shot 2019-04-12 at 5.27.55 PM.png
>
>
>
> On Fri, Apr 12, 2019 at 7:48 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> You can just multiply the output
Hi Mustafa, why not just run recon-all on the data you have and see
whether it looks ok?
On 4/15/19 7:06 AM, mustafa amin wrote:
> External Email - Use Caution
>
> Hi Bruce,
>
> I’ve talked to the MRI operator and she told me that the best thing to do the
> MP-RAGE protocol is doing the
Unfortunately, it usually means that you need to go in and manually fix
the problems that you are seeing. Probably the best thing is to look at
the aseg.presurf.mgz to see how the WM lesions are getting labeled. You
may have to go in an label them manually. Can you upload a case or two
here ftp
Can you send a picture?
On 4/16/19 2:07 PM, Rachel Hoel wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Developers,
>
> Our study is using the longitudinal processing pipeline with version
> 6.0. We have one subject where there is a hyperintenisty in the right
> temporal lobe
al-xyz requires a volume input, but the
> instructions don't include one, so it you run it exactly like it is there
> you'll get an error.
>
> Thanks,
> Katie
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-
Are they exactly the same? Try
mri_diff file1.mgz file2.mgz
I would not expect them to be all that different, just a few voxels here
and there
On 4/16/19 3:47 PM, Sam W. wrote:
>
> External Email - Use Caution
>
> Hi,
> In a Freesurfer help webpage it says that to convert an image (eg
>
Can you upload the functional volume to
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
Let me know when it is there and what the file name is
On 4/16/19 5:55 PM, Mcnorgan, Christopher wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> For some reason I’m having a problem replyin
; the ribbon and it shows that those label voxels are not inside the ribbon.
>
>
>
> Screen Shot 2019-04-16 at 1.30.01 PM.png
>
>
>
>
> Screen Shot 2019-04-16 at 1.28.47 PM.png
>
> On Tue, Apr 16, 2019 at 10:48 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harv
> the ribbon and it shows that those label voxels are not inside
> the ribbon.
> >
> >
> >
> > Screen Shot 2019-04-16 at 1.30.01 PM.png
> >
> >
> >
> >
> > Screen Shot 2019-04-16 at 1.28.47 PM.png
>
can you send the full terminal output of the mri_surf2vol command?
On 4/17/19 5:59 AM, Loïc Daumail wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am currently trying to use mri_vol2surf on my bold data. I typed
> this commandline :
> "
> mri_vol2surf --mov
>
Sorry, I've been having problems getting the patch together because of
difficulties compiling version 6 on centos 7. Should be ready today.
On 4/16/19 11:43 PM, Alvarado,Luis R wrote:
>
> External Email - Use Caution
>
> Dear Freesurfers,
>
> I just read the page about “Fixing of Morphome
can you be more specific?
On 4/17/19 12:20 PM, Alvarado,Luis R wrote:
>
> External Email - Use Caution
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_
thing. I
> was just wondering if I was missing something.
>
> Thank you,
>
> Luis R. Alvarado
>
> On 4/17/19, 11:26 AM, "Greve, Douglas N.,Ph.D."
> wrote:
>
> Sorry, I've been having problems getting the patch together because of
> diff
C contrast.mtx --o
> lh_NHPT_T1T2_12CMT_allbrain
>
>
> Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> what is your command line?
>
> On 4/11/19 3:53 PM, TMS lab wrote:
> >
> > External Ema
s are failing.
>>
>> Thanks,
>> Chris
>>
>> /**********
>> * Chris McNorgan
>> * Assistant Professor
>> * Department of Psychology
>> * University at Buffalo,
>> * The State University of New York
>> * http://ccnlab.buffalo.edu/
urv.fsavg.mgh --fsgd
> age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o
> lh_NHPT_T1T2_12CMT_allbrain
>
>
> Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
>
h label2vol should definitely be used instead of vol2vol?
> Best regards,
> Sam
>
>
> On Tue, Apr 16, 2019 at 10:12 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Are they exactly the same? Try
> mri_diff file1.mgz file2.mgz
>
If you want to transfer a segmentation, then it is better to use
mri_label2vol with the --seg option. Run it with --help to get examples.
Probably even better is to transfer your functional to anatomical space
(mri_vol2vol) so that it is in registration with the anatomical;
transferring it to a
Use mri_label2vol with --fill-ribbon. Note that you can use this to
convert the aparc.a2009s into the volume space, then use something like
mri_binarize to extract the labels you want.
On 4/16/19 7:52 PM, Sam W. wrote:
>
> External Email - Use Caution
>
> Hi,
> I created a series of labe
oesn't it? And the
> mri_label2vol command above does the registration from seg to
> example_func, which is the opposite direction to what reg.dat encodes.
> Could you clarify that to me please?
> Best regards,
> Sam
>
>
> On Wed, Apr 17, 2019 at 11:27 PM Greve, Douglas N
This often happens because the white surface is in accurate and fixing
the white surface will fix the pial. Is the white surf ok? Sending pics
would be helpful
On 4/18/19 1:28 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> I asked about this a
On 4/19/2019 11:35 AM, Wang, Xiaoyu wrote:
External Email - Use Caution
Dear FreeSurfer Experts,
We are trying to compare the early onset hemisphere vs Late onset hemisphere of
PD patients.
I am trying to use Xhemi in order to reorganize all early onset hemisphere to
the left hemi
look at mri_segstats. Run it with --help to get examples. Note that if your
input volume has multiple frames, you can use --avgwf to get means of all the
frames
On 4/19/2019 4:46 PM, Sims, Sara A (Campus) wrote:
External Email - Use Caution
Hello!
I have a surface overlay that I want to
I'm not an excel expert, so there might be a way to get excel to create the
fsgd file for you. I would probably export it as a text or csv file, then use
matlab or shell scripts to create the fsgd file.
On 4/19/2019 5:49 PM, Amrita Bedi wrote:
External Email - Use Caution
Hi Freesurfer
fer-boun...@nmr.mgh.harvard.edu>
on behalf of "Greve, Douglas N.,Ph.D."
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Saturday, April 20, 2019 at 12:07 PM
To: "freesurfer@nmr.mgh.harvard.edu"
You will have to go through a few steps.
1. Sample your labels onto the surface with
mri_vol2surf --mov yoursegmentation.mgz --regheader --s subject --hemi lh
--interp nearest --o lh.mysegmentation.mgz
2. Convert the surface-sampled segmentation to an annotation using
mris_seg2annot. Run it with
How did you create the label? Is it a surface-based label? Ie, does it have
valid vertex indices as the first item in each label point in the label file?
On 4/24/2019 2:44 AM, Nillo, Ryan Michael R wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am using the code bel
The "locale" error is probably not a problem. Does
/media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white exist? What operating
system are you using?
On 4/24/2019 6:41 AM, Javier Navas wrote:
External Email - Use Caution
Dear freesurfer experts,
I want to create an annot from the out
I don't think there was a file attached. Have you been able to processes any
subjects in FreeSurfer? Or does it fail in this way on all subjects?
On 4/24/2019 4:59 AM, Ebru Ayyürek wrote:
External Email - Use Caution
Hi FreeSurfer Developers,
I'm attempting to perform a full recon-all
freeview. The mri_surfcluster worked well in the past.
> However, I recently downloaded the fspalm and the mri_surfcluster
> attached for the fspalm. I do not know if it could interfere...??
>
> I'm using Ubuntu 18.04 x86_64
>
> El mié., 24 abr. 2019 a las 19:13, Greve
Don't use --best anymore, it is depricated. There should be no need to specify
an initialization (unless it is to initialize it with the header geometry).
Under the hood, it will use mri_coreg (a shameless copy of spmreg).
On 4/24/2019 7:07 PM, Pfannmoeller, Joerg Peter wrote:
Hello,
I have a p
can you send command line and terminal output?
On 4/25/19 10:37 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear freesurfer experts,
>
> I am running the rbv pvc correction on a mac system and encountered
> the following error.
>
> mghRead(/Volumes/DATA_PETMR/
On 4/25/19 10:54 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I am reading your work 'False positive rates in surface-based
> anatomical analysis' and having several questions about multiple test
> correction in mri_glmfit-sim:
>
> 1. The permutati
0.01 --rbv --o
/DATA_PETMR/data_donatienne/Boston_final_analysis/VT/Vt_all/${word}/PVC/gtmpvc.output.spmreg
--no-rescale
Kind regards
Donatienne
Op do 25 apr. 2019 om 17:44 schreef Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:
can you send command line and terminal output?
On
.
Op vr 26 apr. 2019 om 17:08 schreef Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:
Does that file actually exist? It seems to think that the subject name is
"unknown", which is probably not right. How did you create suv.reg.lta? That
file should have the name of the sub
You can use --slicedirection to get the slice direction (it will also
get printed out by just running mri_info on a file). What do you mean by
the image origin?
On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> This is not directly r
Can you send your command line (with -cw256) and the recon-all.log file?
On 4/23/19 6:54 AM, Anik Dar wrote:
>
> External Email - Use Caution
>
> Hello All,
>
> I am running recon-all highres on 10 7T MP2RAGE datasets that has been
> skull striped and in two subjects, I get the following
First, create an LTA to go from the orig to rawavg space:
tkregister2 --noedit --mov orig.mgz --targ rawavg.mgz --reg deleteme.dat
--ltaout reg.orig-to-rawavg.lta --regheader
Then concatenate with the input volume lta, eg,
mri_concatenate_lta -invert2 reg.orig-to-rawavg.lta 001.lta
reg.orig-to-0
000 1.
>
> In that transform the last column indicates the image's origin. However, I
> was unable to find the relation between the information available in the
> DICOM header and this transform.
>
> Best,
> Falk
>
>
> -Ursprüngliche Nachricht---
If you have them in nifti format, you can use afni or fsl (we don't have our
own motion correction)
On 5/3/2019 1:18 PM, Shane Schofield wrote:
External Email - Use Caution
Hi Freesurfer Team,
How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean
image for moti
obtained the time course from a unique region
> expressing the merging of thalamic regions (i.e. 8121 plus 8122 plus
> 8123), which is the options that should I added to mri_segstats?
>
>
>> Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D."
>> ha scritto:
The --in_orientation should work. The RAS coordinates will reflect subject
space (which is probably what you want) and not scanner space.
On 5/7/2019 11:27 AM, Caspar M. Schwiedrzik wrote:
External Email - Use Caution
Hi!
I have data acquired on a Siemens scanner with head first-prone.
You can use aparcstats2table, just specify -p aparc.pial
On 5/8/19 11:17 PM, Ting Li wrote:
> External Email - Use Caution
>
> Dear Freesurfer Expert,
>
> Is there a way to get the aparc.pial.stats in one command like
> aparcstats2table?
>
> Thanks a lot!
>
> Best regards,
> Ting
>
> _
Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> Im Auftrag von Greve, Douglas
> N.,Ph.D.
> Gesendet: Freitag, 3. Mai 2019 17:31
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] Primary slice direction and image origin?
>
> You can get the ima
Are the parcels in the volume or on the surface? If in the volume, then use
mri_vol2surf to map them (as a "segmentation") onto the surface, then use
mris_seg2annot to create an annotation file. Run either with --help to get docs
and examples
On 5/10/2019 2:26 PM, Bruce Fischl wrote:
Hi Mahsid
Hi Victor, it might make more sense to use the hires patch that we just
developed last fall
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
there is a README file there with instructions on how to install and use
On 5/10/2019 11:18 AM, Zeng,Victor (BIDMC - Psychiatry) wro
In freeview, it is just an icon above the image window. Click on it and it
should give you a scale bar
On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I am trying to add a spatial scale bar to my cortical maps in tksurfer.
However, as it's mentioned in Freesurfer forum
ge lh inflated -ov sig.nii.gz
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: Fr
I would use the high res stream I made for the HCP
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
On 5/13/19 4:23 PM, Fuller-Deets, Josh (NIH/NEI) [C] wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer users,
>
>
> we have a new Terra 7T scanner and I'm havin
you have to use the output of mri_label2vol in the freeview command
On 5/13/2019 5:02 PM, Sam W. wrote:
External Email - Use Caution
Hi,
After bbregister, I ran mri_label2vol to convert a segmentation file to native
functional space
mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat -
ion with the -f flag in freeview. So how can I convert
the wm surfaces to functional space?
Sam
On Tue, May 14, 2019 at 4:11 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
you have to use the output of mri_label2vol in the freeview command
On 5/13/2019
You can use something like mri_surf2surf --s subject --src-area midsurf --hemi
--trgval lh.area.midsurf
run with --help to get examples
On 5/14/2019 10:42 AM, Bruce Fischl wrote:
Hi Tim
not sure about area (Doug might have something), but for curvature you can do:
mris_curvature -w lh.area.midg
did you check the output? I think it should have the appropriate number of
frames. You can use mri_info to check the dimensions
On 5/13/2019 7:35 AM, Robert Austin Bruce Benn wrote:
External Email - Use Caution
Hi There,
I’m currently trying to run mri_vol2surf on some animal data and
what version of FSL are you running? That program (mni152reg) is just a front
end for running flirt, so you can always run flirt by itself.
On 5/13/2019 8:49 AM, vin rasa wrote:
External Email - Use Caution
Dear Freesurfer Experts!
The idea is to transform freesurfer output in to the M
sorry, I'm not sure what you are trying to do. When you say you would like to
smooth the data then resample, do you mean smooth on the surface? and do you
mean resample to the standard surface or volume space?
On 5/13/2019 11:26 AM, Zhi Li wrote:
External Email - Use Caution
Dear Frees
I created a matlab file called annotval2surfoverlay.m. Does this do what
you want?
surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile)
Example:
I have three annotations
annotnames = strvcat('superiortemporal','insula','postcentral');
with matchine values
anno
There is not a "direct" mask, but you can use
mri_binarize --i aparc+aseg.mgz --csf --o csf.mgz
On 5/14/19 12:05 PM, Yaoshen Yuan wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer team,
>
> I am planning to get the CSF binary mask using Freesurfer. I saw
> previous discussion
ata in the file
> 'fmcpr.odd.sm0.mni305.2mm.nii.gz', is that correct? If so, may I know
> the command to mask the volume and surface fMRI data?
>
> Besides, is that correct about the second question? Thank you very much.
>
> Best wishes,
>
> Lizhi
>
>
> On
-cubic only affects the very first part of the stream, so it should not
affect processing when you re-run after edits
-custom-tal-atlas also only affect the first part of the stream
-qcache should only be run after you have done all of your processing.
If you do not re-run it, then qdec will us
I can't replicate the error (even when using the same subject name), so
I'm not sure what to say. The only think I can think of is that it is
something in your environment that is causing the strangeness. Can
someone you work with run the command to see if the same error happens?
On 5/14/19 5:0
what are MNI surface coords?
On 5/14/19 5:30 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Hello,
>
> We have an anatomical atlas that we have incorporated in the
> FreeSurfer pipeline. Is it possible to convert this voxel based atlas
> into MNI152 surface coordinates? Any
I would run recon-all on the MNI152, then sample the ROIs onto the
MNI152 surface, then transfer them to fsaverage using mris_apply_reg or
mri_surf2surf.
On 5/15/19 1:46 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Hi FS experts,
>
> I am interested in displaying my ROI:
om: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
> N.,Ph.D.
> Sent: Tuesday, May 14, 2019 5:38 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Voxel to Surface Coordinates
>
> KKI SECURITY ALERT
's why I want to smooth in the volume before resampling, I set the
> flag '-fwhm' in preproc-sess as 0, hence it should not smooth the
> data, right?
>
> Best wishes,
>
> Lizhi
>
> On Tue, 14 May 2019 at 13:40, Greve, Douglas N.,Ph.D.
> mailto:dgr...@
Instead of putting control points, you should edit the wm.mgz. BTW, it
looks like some of the control points were not fully in white matter,
which can be problematic.
On 5/14/19 2:27 PM, Rachel Hoel wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Developers,
>
> We're still s
g recon-all on MNI template)?
>
> On Wed, May 15, 2019 at 1:32 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> I would run recon-all on the MNI152, then sample the ROIs onto the
> MNI152 surface, then transfer them to fsaverage using
> mris_a
eeview.
>
>
>
> Ryan Michael Nillo
> Staff Research Associate I
> University of California San Francisco
> Department of Radiology and Biomedical Imaging
>
>> On May 15, 2019, at 1:46 PM, Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu&
You can convert the ROI into a label (mri_vol2label), then "paint" the
label onto the nearest cortex using mri_label2label with the --paint
option. dmax controls the maximum distance, so you'll need to set that
pretty large. You can then load the label onto the surface to see where
it landed.
Can you send the command line and full terminal output?
On 5/16/19 5:17 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi!
> We are getting segmentation fault (core dumped) error when trying to
> run mri_convert on NIFTI files. This is running Freesurfer v5.3 on
>
In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz --ctab-default
...
when you use --annot, you are saying that the input is on the surface.
On 5/17/2019 9:07 AM, Boris Rauchmann wrote:
External Email - Use Caution
Dear Freesurfer community,
I am trying to extract SUV valu
Yes, look in the gtm.stats.dat file. See this page for whichi column you need
to look at
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
On 5/17/2019 12:42 PM, Boris Rauchmann wrote:
External Email - Use Caution
Hi all,
is there a way to easily get the volume stats for all regions
You can also convert, eg, thickness, to mgz
mri_convert lh.thickness lh.thickness.mgz
Then load the mgz in matlab, eg,
th = MRIread('lh.thickness.mgz');
then replace the pixel data with your own
th.vol = YourData;
Then write out the result
MRIwrite(th,'lh.yourdata.mgz');
On 5/19/2019 5:26 PM, Bruc
No, you'll need to change your paradigm file to have two distinct 8 sec
events rather than one 16 sec event.
On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesurfer experts
>
>
> I am making an analysis in Freesurfer version 6 and I have a question
> about the "refeventdur" in mkanaly
Hi Mustafa
> >
> > can you give us some detials? What didn't work? Can you send us the full
> > command line, screen output and recon-all.log?
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 16 May 2019, mustafa amin wrote:
> >
> >
They should be there. Can you send recon-all.log and conf2hires.log files?
On 5/20/19 9:59 AM, Bruce Fischl wrote:
> Hi Victor
>
> the lh.white.{KH} are generated from the lh.white file, so I don't
> think it can have skipped creating it. Was it deleted? Can you double
> check?
>
> Bruce
> On Mo
How did you choose thresholds of 1 and 49.95? In general, you don't need
to set --thmax. If you input is a binary mask, then you should set
--thmin to somethiing below 1 (eg, 0.5)
On 5/20/19 2:40 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to obtain clusters of vertices wh
Can you send the terminal output?
On 5/20/19 8:51 AM, Michal Tanzer wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
> I am having some difficulties in creating annot file for specific ROIs
> using the 2009atlas. When I am using this command, it saves the annot
> but
You will not need to run the entire stream again. Did you run it in
high-res mode? If the volumes are conformed (eg, orig.mgz is 1mm,
252^3), then you do not need to do anything. Otherwise, you will need to
re-run only part of it using the patch and running
recon-all -s subject -segstats -parcs
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