ne. There are
> different options for this command line but I didn't find any option
> to set the color scale to which I want "Color Wheel".
>
> Is there any tool existing allowing to use "Color Wheel" color scale
> by scripting ?
>
> Best,
>
>
depends on what you want in the end. You can do that analysis, but
p-values will be meaningless. Do you just want the difference between
the subject and the group mean? If so, that will work. It should also
give you z-values if that is of intereest
On 7/18/19 2:33 PM, m s wrote:
>
> Ext
Have you looked at the tutorial?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel
On 7/20/2019 4:59 PM, FAST Study wrote:
External Email - Use Caution
Dear Dr. Greve,
Will you please help me learn how to view the output of the paired t-test - via
mri_glmfi
Use mri_binarize --match segid --i aseg.mgz --o mask.mgz
where segid is the segmentation code (eg, left hippo is 17) from
$FREESURFER_HOME/FreeSurferColorLUT.txt
On 7/21/2019 2:09 AM, Dandil dNd wrote:
External Email - Use Caution
Hi Bruce,
Thank you for your reply. I want to create a
There is nothing in the log file that indicates a problem. Was there anything
else printed to the screen? Try running this command to see if it works
cd Users/adomas/Desktop/test/Subj001/scripts
mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
On 7/21/2019 8:54 AM, Adomas Bunevicius
In most of the tools there is an option to invert the matrix before you
apply it. If you save the registration matrix as an LTA instead of DAT,
then most of the tools will figure out the directionality.
On 7/22/19 4:24 PM, Sam W. wrote:
>
> External Email - Use Caution
>
> Hi,
> I would
a-inv
reg.lta
I'd like to output an FSL-style registration matrix because I intend to use
some of FSL tools.
Thanks for your help!
Sam
On Mon, Jul 22, 2019 at 10:35 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
In most of the tools there is an option to invert the m
FreeSurfer has its own permutation software
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
We also have a handy interface to palm
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 7/27/2019 9:33 PM, Mark Wagshul wrote:
External Email - Use Caution
Grea
the reason and how to cope with that? We cannot normalize
> the volume data to eTIV (as it is not proper), what value should we
> use instead?
> Best regards,
> Agnieszka
>
> sob., 22 cze 2019 o 02:15 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> napisa
> do we implement this in segstats?
>
> Thanks,
>
> Mark
> ___
> Mark Wagshul, PhD
> Albert Einstein College of Medicine
> Bronx, NY
>
> Sent from my iPhone
>
>> On Jul 18, 2019, at 11:50 AM, Greve, Douglas N.,Ph.D.
>> wrote
houldn't it?
> Now I ran lta_convert --inlta reg.lta --invert --outfsl
> freesurfer-to-diff.mat. I believe freesurfer-to-diff encodes the
> transformation from freesurfer space to diffusion space, is that correct?
> Best regards,
> Sam
>
> On Tue, Jul 23, 2019 at 3:15 AM Greve,
did you run recon-all -qcache ... on all your subjects?
On 7/25/19 3:35 PM, Renew Andrade wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts:
> I am processing in qdec 3 subjects with the GUI and I have this
> terminal output.
>
>
> Error in Analyze: Couldn't open
> /App
The label file has much less info than the surface file (eg, does not
have neighborhood relations). mri_label2vol requires that a full surface
file be provided. It might not be obvious because it usually finds the
surface based on the subject name.
On 7/25/19 3:29 PM, Sam W. wrote:
>
>
running the
> simulations. Your thoughts?
>
> Thanks for the help.
>
> Mark
> ___
> Mark Wagshul, PhD
> Albert Einstein College of Medicine
> Bronx, NY
>
> Sent from my iPhone
>
> On Jul 28, 2019, at 4:11 PM, Greve, Douglas N.,Ph.D.
> mai
ll design_ttest2 for producing contrast and design matrix?
>
>
>
> Best,
>
> Reza
>
>
> *From:* Greve, Douglas N.,Ph.D.
> *Sent:* Wednesday, July 17, 2019 5:31:27 PM
> *To:* Reza Rahmanzadeh; Freesurfer support list; gr...@nmr.mgh.harvard
in mris_preproc? Is --projfrac-max min max
> delta just the same?
>
>
> Best,
>
> Reza
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Reza Rahmanzadeh
>
> *Sent:
Does it run correctly outside of Nipype?
On 7/29/19 10:50 AM, Pratik Kashyap wrote:
>
> External Email - Use Caution
>
> Hello experts,
>
> I'm running recon-all by wrapping it in a Nipype workflow.
> (cmdline:
> recon-all -all -i {data/T1_files(iterfield)} -openmp 64 -sd . -s seg )
> The
Hi Lauri, try example 8b in
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
I just created it, so please let me know if something seems not right:)
doug
On 7/29/19 1:41 PM, Lauri Tuominen wrote:
> External Email - Use Caution
>
> Dear Freesurfers,
> I am targeting the MNI152
problem with mris_proproc to compute the
> average.
>
> What should i do?
>
> Thanks,
> Reza
>
> On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>> one computes the average, the other computes the maximum
Have you seen this tutorial?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
it uses permutation (which does not work with weighted least squares),
but you could change it to use the old monte carlo stuff.
On 7/29/19 2:15 PM, FAST Study wrote:
>
> Externa
look in subject/scripts/build-stamp.txt
you should see something like
freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb
On 7/29/2019 6:40 PM, FAST Study wrote:
External Email - Use Caution
Hi!
I am re-running all recon-all using version 6.0. I was running a full list of
subje
Hi Brian, I'm looking at your data. For the most part, it looks like the
surface placement is accurate. I do find a few places where the white
surface "leaks" into the cortex like in the attached picture just to the
left of the cursor. Is this the type of thing you are worried about? If
not, p
I don't know anything about fsleyes or fsl command to extract data. In
FS, you can use mri_segstats after resampling the PET to the anatomical
space (mri_vol2vol). Use the PET as the --i and the aseg+aparc as the
--seg. Alternatively, you could use PETsurfer
https://surfer.nmr.mgh.harvard.edu/f
I don't think it will take 20h, probably more like 10-12h, so that's
only 1.5 years:). Most people who are running it that many data sets
have access to a computational cluster (on ours it would only take a few
weeks). Alternatively, you can try buying cloud-based computational
power (eg, amazo
’t write -fsgd argument. Is this way correct?
>
>
> Thanks,
> Reza
>
>> On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D.
>> wrote:
>>
>> Oh, I guess that's a problem! I've created a new version here
>> https://gate.nmr.mgh.harvard.edu/s
rks well for NODDI and i entered the correct registration file into
> mris_preproc.
>
>
> Thanks,
>
> Reza
>
>
> *From:* Reza Rahmanzadeh
> *Sent:* Tuesday, July 30, 2019 6:17:22 PM
> *To:* Greve
Each PVR adds a single column to the design matrix. In a two group design, this
can make it tricky to set up. Let's say you have 10 of group1 and 20 of group2.
You will need to create two PVR files, each with 30=10+20 frames. In the first
one, the first 10 frames will be cortical thickness (or a
If you look in the recon-all.log file for any subject, you will see a
mri_aparc2aseg command line. YOu can use that specifying your annot and the new
output name.
On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote:
External Email - Use Caution
Dear experts,
I have a segmentation file of
You'll have to sample your volume-based segmentation onto the surface using
mri_vol2surf (you might have to play with the projection fraction). Then use
mris_seg2annot. If you run it with --help, you will get an example. The tricky
part is getting the color table set up correctly
On 8/1/2019 4:
,
Reza
From: Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, July 31, 2019 12:50:45 AM
To: Reza Rahmanzadeh; Freesurfer support list
Cc: gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] need
THe last command run is
ln -s lh.white.preaparc.H lh.white.H
So I'm guessing that the error comes when the symbolic link is created (and it
would not be captured in recon-all). That link is the first created in the
stream, so it would not necessarily have shown itself before then. Try this:
cd /
can you be more specific? What kind of effects?
On 8/4/2019 4:29 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear experts,
Knowing the size of the effects on volume-based data, does anyone would know a
way to estimate the size of the effects on surface data?
Best,
Matth
the name of the program in 5.3 is mri_cor2label
On 8/5/2019 11:41 AM, Alshelh, Zeynab wrote:
Hi freesurfers,
I am currently using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and I
need to run $mri_vol2label which I have been informed works with fs v6.0. Is
there any way I can use this com
can you give more info on the error? Eg, command line, terminal output, log file
On 7/31/2019 6:55 PM, Gregory Mierzwinski wrote:
External Email - Use Caution
Hello,
Even though this is an old post, the entire solution to this has not been
posted and I couldn’t find it anywhere.
I hit
values are zero. My registration for bbregister is fine
and i wrote my mris_preproc the same as MWF maps.
Thanks,
Reza
From: Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, August 2, 2019 3:35:45 PM
To: Reza Rahmanzadeh; Free
smoothing to apply before statistical analysis. I
know the FWHM to apply to a volume-based study but wonder what should be apply
regarding the surface-based study?
Best,
Matthieu
On 04/08/2019 22:53, Greve, Douglas N.,Ph.D. wrote:
can you be more specific? What kind of effects?
On 8/4/2019 4:29 PM
Use mri_vol2surf, something like
mri_vol2surf --mov norm.mgz --hemi lh --projfrac 0.5 --regheader subject --o
lh.norm.mgz
On 8/5/2019 11:57 AM, Axelson, Eric D wrote:
External Email - Use Caution
Is there a way to extract the gray matter intensity value at each vertex of a
surface file
You should untar your tar file so that the individual dicoms are available.
You will see many (more than 150) dicom files.
If you know for sure that there is only a single T1 volume in the group, you
can just run
recon-all -s yoursubjectname -all -i path/to/dicom/one_dicom_file
where one_dicom
ip between amyloid-thickness in group2 regressing out age
and education?
On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Each PVR adds a single column to the design matrix. In a two group design, this
can make it tricky to set up. Let's say you
what is your registration command?
On 8/2/2019 12:17 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I have a subject that the registration is not done correctly in two runs (run
12 and run 15) .
The tkregister-sess values for this subject is shown below.
Subject 1 10 0.2628
Subject 1
<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: Monday, August 5, 2019 1:01:07 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu
ory of Early Experience and Development (LEED)
> bdbiek...@uh.edu
> brian.biek...@times.uh.edu
>
> ____
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D.
> [dgr...@mgh.harva
.rhmgxctx.fsaverage.sm05.zero.nii.gz \
--pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
That mostly looks good.
I would suggest is to chang
contrasts are
correct, I think the commands should be right.
Best,
Paul.
Sent from my Samsung Galaxy smartphone.
Original message
From: "Greve, Douglas N.,Ph.D."
<mailto:dgr...@mgh.harvard.edu>
Date: 2019-08-05 15:52 (GMT-05:00)
To: freesurfer@nmr
rh.pet.thickness.glmdir
contrast = 0 0 0 0 0 0 -1 1
On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
It still looks like you are using a group specific input (--y). The input
should be a simple file with both groups (same input as you would use w
t;
> The outputs of all three steps are attached.
>
>
>
> Looking forward for your helps
>
> Reza
>
>
>
>
>
>
>
>
> *From:* Greve, Douglas N.,Ph.D.
> *Sent:* Monday, August 5, 2019
ed.avg.mgh --tval lh.NDI_inflated.avg.05.mgh
>>
>> 3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C
>> contrast --fsgd fsgd.fsgd --cortex --glmdir
>> lh.NDI_inflated.avg.05.glmdir
>>
>>
>>
>> The outputs of all three steps are
Can you send command lines? Also, are you using the built-in permutation
tool or trying to do something outside of FS?
On 8/6/19 8:40 AM, Daliah Ross wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer experts,
>
> I have a couple of questions regarding mri_segstats tool for an
> a
You should edit the wm.mgz. In these places, the WM will be labeled as
non-WM. Just erase the mislabeled voxels.
On 8/6/19 6:31 PM, Caroline Chwiesko wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer experts,
>
> I wrote a previous email about my issue that in many of my subjec
Then re-run with
recon-all -s subject -autorecon2-wm -autorecon3
On 8/6/19 6:42 PM, Greve, Douglas N.,Ph.D. wrote:
> You should edit the wm.mgz. In these places, the WM will be labeled as
> non-WM. Just erase the mislabeled voxels.
>
> On 8/6/19 6:31 PM, Caroline Ch
ps, and I meant to say that the non-WM will be labeled as WM.
On 8/6/2019 6:44 PM, Douglas N. Greve wrote:
> Then re-run with
> recon-all -s subject -autorecon2-wm -autorecon3
>
>
> On 8/6/19 6:42 PM, Greve, Douglas N.,Ph.D. wrote:
>> You should edit the wm.mgz. In these p
rface based pet analysis and mutlimodal analysis (pet
> and thickness), should i use --3spaces?
> Thank you.
>
> best,
> Paul
>
> On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> I think there is still
for NDI maps?
>
> Thanks,
> Reza
>
>> On 7 Aug 2019, at 17:05, Greve, Douglas N.,Ph.D.
>> wrote:
>>
>> Every vertex of every subject is 0 in lh.NDI_inflated.avg.05.mgh
>>
>>> On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:
>>>
>>>
ERROR: no voxels found in the mask
>>>>>> make sure at least one voxel has a non-zero value for each input
>
> Reza
>
> On 7 Aug 2019, at 17:11, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>> no idea until you tell me what
If you do not specify --projfrac-avg, does it come out as non-zero? If
so, I would think that it is a problem with the registration. Have you
checked the registrations?
On 8/7/19 11:25 AM, Reza Rahmanzadeh wrote:
> External Email - Use Caution
>
> It means that for any given subjects i’
gt;
>> On 7 Aug 2019, at 17:29, Greve, Douglas N.,Ph.D.
>> wrote:
>>
>> If you do not specify --projfrac-avg, does it come out as non-zero? If
>> so, I would think that it is a problem with the registration. Have you
>> checked the registrations
er-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.
> Sent: Tuesday, August 6, 2019 12:56 PM
> To: freesurfer@nmr.mgh.harvar
Hi Heidi, I'm not sure I understand what you are trying to do. Can you
elaborate? What do you mean that you do not have statistical info any more? It
is unusual to smooth p-values. Probably you should apply smoothing before your
analysis
On 8/9/2019 2:46 PM, Jacobs, H (NP) wrote:
Exter
When you say deconvolution, what do you mean exactly? There is an FIR model
(finite impulse response) that will extract the hemodynamic response without
any assumptions, ie, the signal average at stimulus onset, the signal average
at 1TR post onset, the signal average at 2TR post onset, etc.
On
d for multiple comparisons at a voxel (rather than cluster) level
(perm.th40.abs.sig.voxel.mgh). There is no summary file for it.
Best,
Paul
On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
The 3 spaces is for left hemi, right hemi, and subcortical,
I have not seen that error before. Have you checked the images to make
sure there is nothing strange about them? Eg, some type of artifact?
On 8/13/19 8:12 AM, Z Hessam wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
> I'm attempting to run some of data with recon
1 2 abs --perm-force --cwp 0.05 --2spaces --bg 10 --overwrite
>
>
> On Mon, Aug 12, 2019 at 11:31 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> You will have to click on the vertex you are interested in. The
> value will be -lo
I don't know what the Brainnetome is, but it looks like you have it in
annotation form. I think that command should work. Why are you using
--no-xcerseg? This will cause it to not include extracerebral
structures. Also note that you cannot use arbitrarily small segments
when doing PVC.
On 8/13
I think those should be already sampled on the surface, so you should
not need a registration file
On 8/13/19 5:09 AM, Hang Zeng wrote:
>
> External Email - Use Caution
>
> Dear freesurfers,
> I ran the retinotopy pipline (like preproc-sess, mkanalysis-sess,
> Selxavg3-sess) and now I wa
mary of cluster. Is this correct?
> Paul
>
> On Tue, Aug 13, 2019 at 10:39 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> I don't know that there is much you can do. The PVR is very
> computationally intensive, and it does not surprise me
--no-xcerseg)
> or create a new one and overwrite what is there (--xcerseg)
> or specify your own headseg (--head)
>
> and did not want to override my apas+head.mgz
>
> Thanks,
> Boris
>
> On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.
When you use -gammafit, it automatically sets the time window to 40. If
you really want it at 80, but -timewindow before -gammafit. Do you
really expect the MION hrf to last 80 sec?
On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi!
> I am having d
:
>
> External Email - Use Caution
>
> Hi Doug,
> Thanks for the advice.
> I think the Leite et al. 2002 NeuroImage paper can be interpreted that
> way. See Figure 1 and 2.
> http://pop.cerco.ups-tlse.fr/pdf0609/leite_fp_02_283.pdf
>
> Caspar
>
> On Tue,
Those coordinates are in mni305 space. See this page, case 8
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 8/13/19 1:56 PM, Avi Gharehgazlou wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am conducting a meta-analysis on papers that have looked at local
> gyrifica
oude <mailto:miracoo...@gmail.com>> wrote:
>
> Awesome. thanks a lot for your help. I appreciate it.
>
> Best,
> Paul
>
> On Tue, Aug 13, 2019 at 10:59 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> You can
ize per
> permutation. Thank you for the advice!
>
> Daliah
>
> *Daliah Ross* | dro...@mail.yu.edu <mailto:dro...@mail.yu.edu>
>
> Ph.D. Student, Clinical Psychology with Health Emphasis
> Ferkauf Graduate School of Psychology
> Yeshiva Univer
> extract the regions and mri_mergelabels to merge them and run analysis
> on them.
>
> On Wed, Aug 14, 2019 at 11:59 AM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Do you mean using different ROIs than in the aparc? If you want to
>
sorry, all the previous emails did not make it into this one so I'm a
bit lost. Can you repost with the previous correspondence?
On 8/14/19 1:51 PM, Mahshid Fouladivanda wrote:
>
> External Email - Use Caution
>
> Dear Doug,
> Thanks for your reply. I have used the same command in the
>
I have not seen it before; I've cc'ed Martin in case he has seen it.
Have you checked the underlying data to make sure that there are no
artifacts, etc?
On 8/13/19 8:02 AM, Dylan Nielson wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer folks,
>
> I'm running Freesurfer's longitu
Not ssure what is happening. CAn you send the full terminal output.
Also, remove the --out_type flag. No need to include --surfreg
sphere.reg (but should not hurt anything).
On 8/14/19 12:37 PM, Pratik Kashyap wrote:
>
> External Email - Use Caution
>
> mri_vol2surf --cortex --hemi lh --
You shoul use mri_label2vol with ROI.nii as the --seg input. How do you
know that --regheader is right?
On 8/15/19 3:13 PM, Rihana Rayan wrote:
>
> External Email - Use Caution
>
> Dear FS users,
> I have performed recon-all on structural data and created ROIs (using
> mri_binarize), I w
The algorithm in v6 is not as you describe. The function below is based
on Anderson Winkler's (cc'ed) work.
/*!
\fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
\brief Compute vertex-wise volume based on dividing each obliquely
truncated
trilateral pyramid into three tetrahedra. Based on A
If there is no interaction between F/R and Active, then there should not be any
theoretical difference between the two analyses, except that FR combined will
be slightly more powerful since it has one more degree of freedom. You should
first use the uncombined model to look for an interaction, a
Did you check the registration (tkregister-sess)? My guess is that the partial
field of view messed up the registration. If so, you can probably get around
this by adding -init-header to preproc-sess
On 8/19/2019 8:11 AM, Hang Zeng wrote:
External Email - Use Caution
Hi Freesurfers,
w
It looks like your SUBJECTS_DIR is set to the wrong place. It should be set to
the folder where ever your subjects (eg, PT1_01) are
On 8/19/2019 4:45 AM, 310913949 wrote:
External Email - Use Caution
Hi FS Experts,
I meet some problem when I use QDEC for Group analysis. When
between
> tkregister view and freeview of the same patient.
> What may be the reason and how to cope with that? We cannot normalize
> the volume data to eTIV (as it is not proper), what value should we
> use instead?
> Best regards,
> Agnieszka
>
> sob., 22 cze 20
You should remove the --l argument. That is incompatible with --ldir.
On 8/19/19 5:50 PM, Rachel S wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer community,
>
> I was trying to use mris_label2annot to generate annotation file, my
> commands are:
>
> mris_label2annot --s p6 --h
I'm not sure I understand. Can you elaborate?
On 8/19/19 2:43 PM, Hopkinson, Casey E wrote:
> Hello!
>
> I am trying to generate significance maps for a paired-difference
> analysis of cortical thickness using multiple pairs of siblings, and
> was wondering if there is a way to incorporate the f
were labeled.
What could be the problem? Thank you.
Best regards,
Rachel
Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>
于2019年8月19日周一 下午6:07写道：
You should remove the --l argument. That is incompatible with --ldir.
On 8/19/19 5:50 PM, Rachel S wrote:
>
> External
There is no file attached. Can you send?
On 8/21/2019 10:25 PM, liuxingze1993 wrote:
External Email - Use Caution
Hello， Dear FreeSurfer Developers,
I’m a doctoral student from Xiangya 2nd Hospital of Central South University,
and also a beginner to FreeSurfer. I'm attempting to follow
Yes, it does everything without regard to age or gender. The full processing
stream is pretty complicated, but it does segment various structures (white
matter and various GM structures)
On 8/22/2019 4:02 PM, Carissa Liana Grijalva wrote:
External Email - Use Caution
Hello FreeSurfer S
05 (fsaverage) space...
Will you please clarify this for me?
Thanks so much,
Avi
On Tue, Aug 13, 2019 at 6:36 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Those coordinates are in mni305 space. See this page, case 8
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSy
.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: Monday, August 19, 2019 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harva
You can use samseg in the development version. Keep in mind that it is somewhat
unstable. Make sure to give it an mgz and not a nifti or mgh file
On 8/23/2019 2:51 PM, Jared Nielsen wrote:
External Email - Use Caution
I've seen some previous posts about a measure of extra cerebral CSF
, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
You shoul use mri_label2vol with ROI.nii as the --seg input. How do you
know that --regheader is right?
On 8/15/19 3:13 PM, Rihana Rayan wrote:
>
> External Email - Use Caution
>
> Dear FS users,
> I have p
unning:
mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from f-in-anat.mgh...
/usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed
Thanks
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D."
<mailto:dgr...@mgh.harvard.ed
You should bring up the T2* with the surfaces. Is it possible that the
T2* just did not include that particular bit?
On 8/26/19 10:38 AM, Sackl, Maximilian wrote:
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I was trying to perform a GLM fit with T2* data, projected on
Any ideas?
>
> On 26.08.2019 16:59, Greve, Douglas N.,Ph.D. wrote:
>> You should bring up the T2* with the surfaces. Is it possible that the
>> T2* just did not include that particular bit?
>>
>> On 8/26/19 10:38 AM, Sackl, Maximilian wrote:
>>>Ext
Actually, the wiki page is not quite right. For a simple interaction between
age and weight, you would need to create a new regressor = age*weight, then set
the contrast to [0 0 0 0 0 0 1]. If you want an interaction between group, age,
and weight, then you would need two new regressors, age*we
correct
On 8/27/2019 11:28 AM, Zhi Li wrote:
External Email - Use Caution
I see. Hence I cannot set the contrast of interaction between two covariates if
I do not create the interaction term by myself, right?
On Tue, 27 Aug 2019 at 10:53, Greve, Douglas N.,Ph.D.
mailto:dgr
It is showing
b = g2 - g1
so negative means that g1 > g2
On 8/28/19 1:59 PM, Barletta, Valeria wrote:
>
> Forgot to report my contrast matrix:
>
> -1 1 0 0
>
>
> Thanks,
> Valeria
>
> *From:* Barletta, Valeria
> *Sent:* Wedn
recon-all does not do so well with data at 0.5mm. I created a high-res
patch for version 6.0 as part of my support fo r the HCP. You can get it
here https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp
this shold work much better.
On 8/27/19 10:15 AM, Giovana dos Santos Cover w
le.
>
> Thanks
>
> Stefano
>
>
>> Il 26 agosto 2019 alle 20.02 std...@virgilio.it ha scritto:
>>
>> Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command
>> runs fine.
>>
>> How can I convert into the functional space the
You can download dev from here
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
On 8/26/19 1:01 PM, Westeneng, H.J. wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> It has previously been reported that vertex 40969 is the same as
> vertex 0, which creat
You can use mri_vol2label. Run it with --help and make sure to use the
--surf option
On 8/27/19 8:32 AM, Nillo, Ryan Michael R wrote:
> External Email - Use Caution
>
> Hello FreeSurfer users/developers.
>
> I manually created a binary overlay file on the pial surface. I am interested
701 - 800 of 1298 matches
Mail list logo
