External Email - Use Caution
Hello,
Any idea how to solve this problem? I have tried the suggested solutions on
the archive, that's Demean and Rescale but to no avail.
I have attached the necessary files in the email below.
Many thanks,
Miracle
mri_glmfit command: mri_glmfit --
External Email - Use Caution
Hello,
Please, can someone answer my questions regarding the along-tract stats
using mri_glmfit and mri_glmfit-sim with permutation for version 7.2.
1) I ran it and I found a significant negative association between FA and
clinical score (see attached
External Email - Use Caution
Hello,
I have questions regarding the along-tract stats using mri_glmfit and
mri_glmfit-sim with permutation for version 7.2.
1) I ran it and I found a significant result (see attached summary file)
where I expected/found a negative association betwee
External Email - Use Caution
I have a similar question to this unanswer one (see link)
https://secure-web.cisco.com/1TPpYYjX_nTrm6lqczxoG15eSKbWRPZCXEekOMWT-xtyurpqfBqaFyz4aiSqrY42eu_2JI_dWX-HNfM9jWT5eTLES0zDZCVeGrslztLwHYrbkr_R08eoTG2wWnG2Be3lJlA5KOn3C00RFTWSpD7jyXDn6V0cmzukr2a1BZ
, 2023 at 11:51 AM miracle ozzoude
wrote:
> Hello Doug,
>
> Thanks for the quick response. I did see the error. However, I specified
> doss in the mri_glmfit command and my mtx looks accurate as indicated
> above. Does that mean it can only work with dods? The reason I'm using 2
&
use I want to regress out the effect of sex. However, the
recommended way to do it in fsgd is to create a class for it and I only
have 3 males.
Is there a workaround for this?
Many thanks.
On Fri, Dec 30, 2022 at 6:37 PM miracle ozzoude
wrote:
> Hello,
>
> I have 2 groups (group 1 = 3 me
External Email - Use Caution
Hello,
I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like
to regress out the effects of groups + other variables by using doss.
However, whenever I specify doss with the mri_glmfit command, it gives me
an error message (see belo
External Email - Use Caution
Never mind. Solved it.
On Mon, Sep 26, 2022 at 1:16 PM miracle ozzoude
wrote:
> Hello,
>
> I am trying to run TRACULA using FreeSurfer version7.2. I followed the
> instructions on the tutorial website for cross-sectional study with 1
External Email - Use Caution
Hello,
I am trying to run TRACULA using FreeSurfer version7.2. I followed the
instructions on the tutorial website for cross-sectional study with 1 scan
(see link below). However, I keep getting "intrareg:Undefined variable"
error whenever I run the fi
External Email - Use Caution
Great. thanks Doug. I appreciate it
On Thu, Jun 24, 2021 at 12:07 PM miracle ozzoude
wrote:
> Hello,
> I was wondering if anyone has an answer to my question.
>
> Cheers
>
> On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude
>
External Email - Use Caution
Hello,
I was wondering if anyone has an answer to my question.
Cheers
On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude
wrote:
> Hello All,
>
> I was wondering if the Right/Left-Cerebral-White-Matter in the
> aparc+aseg.mgz
External Email - Use Caution
Hello All,
I was wondering if the Right/Left-Cerebral-White-Matter in the
aparc+aseg.mgz contains WM hypointensities.
mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
--ctab FreeSurferColorLUT.txt
Best,
Paul
External Email - Use Caution
Hello All,
I was wondering if the Right/Left-Cerebral-White-Matter in the
aparc+aseg.mgz contains WM hypointensities.
mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
--ctab FreeSurferColorLUT.txt
Best,
Paul
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 parcellation with --ctab only reports on non-empty
segmentations. I want
External Email - Use Caution
Hello Experts,
I did like to extract wm whilst retaining the label ids. I tried
mri_extract_labels but it didn't work.
Any help would be appreciated.
Many thanks,
Paul
___
Freesurfer mailing list
Freesurfer
a diagonal weighing matrix.
During the estimation stage, the forward model is inverted to
solve for B:
B = inv(X'W'*W*X)*X'W'y
3) Lastly, how do I extract the beta-values after running mri_glmfit-sim
without matlab?
Many thanks,
Paul
On Tue, Feb 23, 2021 at 12:37 AM mi
External Email - Use Caution
Hello Experts,
I've a question about mri_glmfit. I want to investigate the association
between thickness and neuropsychiatric syndromes, controlling for age and
cognition. Which model below is mri_glmfit performing?
Model 1
neuropsych syndromes ~ age
} --o ${gtm_out_nopvc} --rescale ${nr}
--replace 29 3
On Fri, Feb 5, 2021 at 1:45 PM miracle ozzoude wrote:
> Hi Doug,
>
> I followed the processing workflow as described on the PETSurfer wiki and
> gtmseg.mgz was created, but included a warning for only one of my subjects:
>
>
External Email - Use Caution
Hi Doug,
I followed the processing workflow as described on the PETSurfer wiki and
gtmseg.mgz was created, but included a warning for only one of my subjects:
WARNING: segid 29 Left-undetermined tissue type is not set
Writing output file to /ID/mri/g
External Email - Use Caution
Nevermind. I didn't see your initial reply Doug. Thanks alot.
Best,
Paul
On Wed, Dec 2, 2020 at 1:35 PM miracle ozzoude wrote:
> Any help with this will be greatly appreciated.
> Thanks.
>
> -- Forwarded message ----
External Email - Use Caution
Any help with this will be greatly appreciated.
Thanks.
-- Forwarded message -
From: miracle ozzoude
Date: Fri, Nov 27, 2020 at 9:28 AM
Subject: extracting mask for basal ganglia, deep grey, and centrum semiovale
To: Douglas N Greve
External Email - Use Caution
Hello Experts,
I did like to create a mask for basal ganglia, deep grey matter, and
centrum semiovale. I know how to extract the mask for the first 2 (using
aseg.mgz) however, how do I extract the last one. What mask should I use to
extract the centrum
recommended) for thickness.
best,
paul
On Wed, Sep 30, 2020 at 10:37 AM miracle ozzoude
wrote:
> Thank you very much Doug. I appreciate it. I guess we will have to redo
> our analyses based using permutation and hope the results are the same
>
>
> On Wed, Sep 30, 2020 at 10:
wer is right, see
> https://pubmed.ncbi.nlm.nih.gov/29288131
> We are recommending permutation analysis, see
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> or
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
>
> On 9/30/20
External Email - Use Caution
Hello Experts,
I have a question regarding grey matter thickness map and signal to noise
ratio. Does smoothing of the map increase signal to noise during surface
based cortical thickness analyses? if yes or no, why? This question was
asked by a reviewe
t1.table.dat
>
> where
> ocn.mgh is something like cache.th13.abs.sig.ocn.mgh
> timepoint1.mgh is the stack of timepoint 1 for all subjects
> The output will be a table with subjects on the rows and clusters on the
> columns
>
> On 6/16/2020 12:28 PM, miracle ozzoude wrote:
>
ons to get your clusters?
> If so, then there should be a table with a row for each subject and a
> column for each cluster.
>
> On 6/16/2020 11:03 AM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello,
>
> I ran a pet longitudinal paired t-test an
External Email - Use Caution
Hello,
I ran a pet longitudinal paired t-test analysis with 2 timepoints using
mri_glmfit and I found significant clusters. I want to extract the values
of these significant clusters for each timepoints. How do I go about doing
this?
Thank you.
Best,
;T just set it to 0 when you go to a
> group analysis.
>
> On 12/2/2019 4:48 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello Experts,
>
> I ran the PETsurfer pipeline using AV45 pet and performed pvc using pons
> as reference point. When i looked
External Email - Use Caution
Hello Experts,
I ran the PETsurfer pipeline using AV45 pet and performed pvc using pons as
reference point. When i looked at the gtm.stats.dat file for one of my
subjects, the SUVr for right and left nucleus-accumbens areas were in the
negative (left =
External Email - Use Caution
Hello Experts,
I do have couple questions about using mri_glmfit and mri_glmfit-sim for
this analysis based on the tutorial page.
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
1) Do i have to add any other flags when using mri_glmfit for this
an
External Email - Use Caution
Hello Experts,
I would like to include covariates in the freesurfer repeated anova steps
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. When i
tried including 3 covariates, mri_glmfit complained about "martix is
ill-conditioned".
How
External Email - Use Caution
Hello Freesurfer,
I am trying to run a surface based paired ttest for pet. I started by
running mri_vol2surf for each pet longitudinal subject. However, when i use
mri_concat with --f, --prune, and --paired-diff i get an error
" --paired-xxx specified
:08 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> The 3 spaces is for left hemi, right hemi, and subcortical, so, if you
> are using all three then correct for all 3
>
> On 8/7/19 9:26 AM, miracle ozzoude wrote:
> >
> > External Email - Use Ca
1_pet.nii.gz --pvr
> ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the
> same as the first but with a reversed sign, but it is not necessary since
> we always use unsigned tests and show both signs (but you can still do it).
>
> On 8/5/2019 8:14 PM, miracle oz
fer] Fwd: multimodal analysis (pet and cortical
> thickness relationship) using --pvr
>
> Yes, that contrast is correct.
>
> On 8/5/2019 3:11 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello Doug,
>
> Thanks very much for your help. Your assump
you need a contrast for
> it.
> 3) below is a sample of my fsgd file. are the constrasts correct?
> hard to say without resolving the questions above. You will need to have a
> value in the contrast for each pvr.
>
>
>
> On 8/2/2019 3:56 PM, miracle ozzoude wrote:
>
>
0 -o group2.zeros.mgz
> Then
> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz
> Then create the contrast based on the FSGD, but then add two more numbers,
> one for PVR1 (which tests for the within group correlation), and one for
> PVR2
>
>
> On 8/1/2019 3:14 PM, miracle ozzo
External Email - Use Caution
Please, can anyone help me with this.
Thank you
Paul
-- Forwarded message -
From: miracle ozzoude
Date: Wed, Jul 31, 2019 at 2:11 PM
Subject: multimodal analysis (pet and cortical thickness relationship)
using --pvr
To: Douglas N
External Email - Use Caution
Hello Experts,
I am performing an analysis looking at the relationship between amyloid
uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups
and 2 variables (age and education). I want to run a within group analysis
while regressi
External Email - Use Caution
thanks doug
paul
On Wed, Jul 3, 2019 at 4:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> yes
>
> On 7/3/2019 4:03 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> E.g. if there are 68 RO
f the number of voxels across all ROIs. See
> https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer here for the identity
> of the columns in the gtm.stats file
>
> On 7/3/2019 3:36 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Over the cortex.
>
&
External Email - Use Caution
Over the cortex.
On Wed, Jul 3, 2019 at 2:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> The mean over what area? Whole brain or just cortex?
>
> On 7/3/2019 2:15 PM, miracle ozzoude wrote:
>
> Externa
External Email - Use Caution
Hello Expert,
How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness
from Freesurfer, I want to extract a global/Mean SUVr value for each of my
subjects.
Thank you.
Paul
___
Freesurfer ma
G. Tau is a little trickier, but I think it has
> been used. I think the reference region for tau is still an open question.
> For FDG, people often use pons.
>
> On 3/25/19 10:33 AM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello FreeSurfer,
>
> I
External Email - Use Caution
Hello FreeSurfer,
I would like to know if mri_gtmpvc for PetSurfer is appropriate for Tau
(AV_1451) and FDG pet imaging. Also, is cerebellum a good reference point
for both tracers?
Thanks.
Paul
___
Freesurf
External Email - Use Caution
Hello,
Can i specify a lookup table when using mri_gtmpvc? This is because I have
a non-freesurfer segmentation (MALPEM) and i would like to perform partial
volume on it without having to run freesurfer on the subject for PET
analysis. I have a lookup
External Email - Use Caution
Hello,
How can I convert a csv color lookup table to freesurfer format (.ctab)? My
end goal is to use it to perform partial volume correction for an
atlas/segmentation different from default freesurfer atlas. The atlas has a
color lookup table however,
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Hello FreeSurfer team,
In order to create the longitudinal base after norm.mgz, Is the command
below the right way to end recon-all after creating norm.mgz?
recon-all -s subjectID -autorecon1 -autorecon2 -i T1image -canorm.
Thank you.
Best,
Paul
__
External Email - Use Caution
Hello,
Can anyone help me with this? I think it got lost in the pool of email.
Best,
Paul
-- Forwarded message --
From: miracle ozzoude
Date: Thu, Jul 5, 2018 at 12:23 PM
Subject: error with mri_ca_register in long
To: Douglas N Greve
External Email - Use Caution
Hello All,
When running the longitudinal pipeline for version 6, i encountered this
error " TransformSample: gcam has not been inverted!; Numerical result out
of range". I found a thread with similar error but the problem wasn't
solved.
https://mail.nm
$FREESURFER_HOME/SetUpFreeSurfer.sh
On Thu, May 31, 2018 at 3:33 PM, miracle ozzoude
wrote:
> Hello,
>
> I was able to solve the previous error (not finding the sources.sh)
> however, i have encountered another error (please find the attached
> hippocampal-subfileds-T1.log file). In this
http://cmictig.cs.ucl.ac.uk/
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <
> miracoo...@gmail.com>
> *Sent:* Wednesday, May 30, 2018 9:21:19 PM
> *
;
> Cheers,
>
>
>
> /E
>
>
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl
t; ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude
> *Reply-To: *Freesurfer sup
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude
> *Reply-To: *Free
you using?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac
External Email - Use Caution
Hello,
I am using v6.0 installed on a linux server (via PUTTY) to segment
hippocampal subfields. I downloaded the runtime from this link (
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the
instructions on how to install it ( it
External Email - Use Caution
Hello,
My Mac has v5.3 installed in the default location ( application). However,
whenever I try to install v6.0 in a different location ( desktop) it deletes
the existing v5.3 from application. Any solution to this? I’m trying to run the
brainstem
sure that it and the talairach_with_skull.lta are ok
>
> cheers
> Bruce
>
>
> On Fri, 27 Apr 2018, miracle ozzoude wrote:
>
>
>> External Email - Use Caution
>>
>>
>> Hello FreeSurfer,
>> While running recon-all on a subject, i got e
External Email - Use Caution
Hello FreeSurfer,
While running recon-all on a subject, i got encountered an error during the
watershed step (mri_watershed). How do i fix this problem? I have attached
the recon-all.log and recon-all-status.log files. Thank you
Best,
Paul
recon-all
is wrong with
> the fist subject
>
> On 2/3/18 3:03 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have uploaded the files you requested. Thank you for your help.
>
> Best,
> Paul
>
> On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve
> wrote:
>
>> Can you
;
> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have attached a screen shot of the mask.mgh for both right and left
> hemispheres. Everything looks yellow. I followed the paired t-test tutorial
> on the wiki page (included my scripts, fsgd files, and matrix i
-- Forwarded message --
From: miracle ozzoude
Date: Fri, Jan 26, 2018 at 7:08 PM
Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline
To: Freesurfer support list
Hello Doug,
Thanks for the patience. Here's the output from the terminal when I ran
mri_g
glmfit done
On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve
wrote:
> can you send the terminal output of mri_glmfit?
>
>
> On 01/24/2018 02:52 PM, miracle ozzoude wrote:
> > Hello Doug,
> >
> > I looked at the fwhm.dat and fwhm value = 0. I have attached the
>
put to see what the value is. Also, send the terminal
> output from mri_glmfit (not mri_glmfit-sim)
>
>
> On 01/22/2018 11:43 AM, miracle ozzoude wrote:
> >
> > -- Forwarded message ------
> > From: *miracle ozzoude* > <mailto:miracoo...@gmail.co
-- Forwarded message --
From: miracle ozzoude
Date: Sat, Jan 20, 2018 at 1:56 PM
Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline
To: Freesurfer support list
Hello Doug,
I tried using the MC tables that FS distributed. However, i got an error
about " c
erage/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
--cwpvalthresh 0.05 --2spaces --overwrite
On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
wrote:
> Why are you doing your own MC simulation? You can just use the tables that
> we distribute ...
>
> On 1/17/18 6:12 PM, mirac
s that we
> distribute ...
>
>> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>> Hello Experts,
>>
>> I am running a paired t-test cortical thickness analysis based on the
>> instruction on the wiki page
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAn
Hello Experts,
I am running a paired t-test cortical thickness analysis based on the
instruction on the wiki page (
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the
monte carlo files weren't not created when i corrected for multiple
comparisons. Below are my script, fsgd fil
e from file ./tmp.mri_nu_correct.mni.
> 53099/nu1.mnc
>
> is that file even there?
>
> Best, Martin
>
>
> > On 8. Nov 2017, at 19:56, miracle ozzoude wrote:
> >
> > Hello FreeSurfer,
> >
> > While running base step of the longitudinal pipeline, i
Hello FreeSurfer,
While running base step of the longitudinal pipeline, i got the following
error (please see the rec-all.log file for more details). How do i solve
this problem? Thank you
Best,
Paul
recon-all.log
Description: Binary data
___
Freesurf
Hello Bruce,
I am still waiting on your response or Lilla's. Thank you.
Best,
Paul
On Wed, Oct 18, 2017 at 8:20 PM, Bruce Fischl
wrote:
> Hi Paul
>
> I was waiting for Lilla to respond :)
> Bruce
>
> On Wed, 18 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruc
Hello,
I am trying to run mri_cvs_register on a subject and I got an error (please
see attached log file). Below was the command I used. Thank you.
mri_cvs_register --mov 01091p --mni --step1 --step2 --step3 --outdir
/Users/MiracleOz/Documents/improvervsdeclinermri/01091p/cvs --asegfname
aparc+as
/subcortical volume based analysis
Hi Paul
I was waiting for Lilla to respond :)
Bruce
On Wed, 18 Oct 2017, miracle ozzoude
wrote:
> Hello Bruce,
>
> I wasn't sure if you answered my previous message hence, I'm sending it
> again. Thank you.
>
> Best,
> Paul
&g
Hello Bruce, I wasn't sure if you answered my previous message hence, I'm sending it again. Thank you. Best, Paul -- Forwarded message --From: miracle ozzoude <miracoo...@gmail.com>Date: Sat, Oct 14, 2017 at 3:32 PMSubject: Re: [Freesurfer] cortical/subcorti
-- Forwarded message --
From: miracle ozzoude
Date: Sat, Oct 14, 2017 at 3:32 PM
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
To: Freesurfer support list
Hello Bruce,
Thank you for the response. I was able to look into CVS command and I wrote
a command
.From: miracle ozzoude Sent: Saturday, October 14, 2017 3:32 PMTo: Freesurfer support listSubject: Re: [Freesurfer] cortical/subcortical volume based analysisHello Bruce, Thank you for the response. I was able to look into CVS command and
17 at 12:38 PM, Bruce Fischl
wrote:
> Hi Paul
>
> I guess you could use CVS for this.
>
> cheers
> Bruce
>
> On Sat, 14 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruce,
>>
>> Thank you very much. Can I still general cortical and subcortical maps
>> w
thing
cheers
Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
> Hello Bruce,
>
> Thank you for the response. I meant the latter ( making maps etc). I want to
> do something similar to the subcortical volume based analysis on PETSurfer
> page however, on freesurfer T1. Freesu
pe of analysis by looking at scatter plots of
structure volumes (e.g. hippocampus). Alternatively, you can make maps,
but that opens up all the problems/difficulties of interpretation of VBM.
Which did you mean?
cheers
Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
> Hello FreeSurfer exper
Hello FreeSurfer experts,
I want to perform a whole brain volume based group analysis for cortical
and subcortical regions. That's something very similar to surface based
group analysis for cortical thickness however, for volume. Is there a
tutorial on how to do it? if yes, please can i get the li
, 2017 at 6:01 PM, Douglas N Greve
wrote:
>
>
> On 09/24/2017 02:17 PM, miracle ozzoude wrote:
> >
> >
> > Sent from my BlackBerry 10 smartphone.
> > *From: *miracle ozzoude
> > *Sent: *Friday, September 22, 2017 9:37 PM
> > *To: *Douglas N Greve
> &g
convince
> the script to look for the stats in the *.long.basename directories.
>
> Best, Martin
>
> Am 26.09.2017 um 17:50 schrieb miracle ozzoude:
>
> Hello Freesurfer,
>
> For the longitudinal pipeline, the website/ recon-all -help suggested that
> I calculate the dif
Hello Freesurfer,
For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 1001_Baseline.long.longbase and 1001_Followup.long.lon
-- Forwarded message --
From: miracle ozzoude
Date: Fri, Sep 22, 2017 at 2:17 PM
Subject: longtitudinal pipeline
To: Douglas N Greve
Hello Freesurfer,
For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different on the results from the
.From: miracle ozzoude Sent: Friday, September 22, 2017 9:40 PMTo: Douglas N GreveSubject: Re: sim-sign abs/ cluster summary results confirmationI forgot to send the cluster summary sheet. Here is it.
# Input
-35.9 1.0
-0.00020 1.0 2 entorhinal
13 -2.001 75892 0.47-22.0 -33.4 -11.8 1.0
-0.00020 1.0 1 parahippocampal
On Fri, Sep 22, 2017 at 9:37 PM, miracle ozzoude
wrote:
> Hello,
>
> I ran cortical thickness analyses using the following contrast
Hello Freesurfer,
For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 0001a.long.0001.longbase and 0001b.long.0001.longbase
-- Forwarded message --
From: miracle ozzoude
Date: Thu, Sep 21, 2017 at 11:20 AM
Subject: nu_correct failure
To: Douglas N Greve
Hello expert,
I ran several subjects on FS v6 and they failed on the same stage
(mri_nu_correct.mni and nu_correct). How can I solve this problem
Hello expert,
I ran several subjects on FS v6 and they failed on the same stage
(mri_nu_correct.mni and nu_correct). How can I solve this problem? I have
attache the recon-all.log file for 2 subjects.
Best,
Paul
recon-all.log
Description: Binary data
recon-all.log
Description: Binary data
__
.From: miracle ozzoude Sent: Sunday, September 17, 2017 11:01 AMTo: Freesurfer support listSubject: Multiple comparison, color maps and contrast Hello, I want to run a whole brain cortical thickness analysis and I will like to confirm
Hello, I want to run a whole brain cortical thickness analysis and I will like to confirm some steps. a) for correcting for multiple comparison, I want to use both Monte Carlo and permutations in order to compare the difference. Are these the right commands? Monte Carlo : mri_glmfit-sim --glmdir
Thank you very much Bruce.
Best,
Paul
On Thu, Sep 14, 2017 at 4:02 PM, Bruce Fischl
wrote:
> I mean there will be no subsequent command that turn of the use of control
> points in the aseg
>
>
> cheers
> Bruce
>
>
> On Thu, 14 Sep 2017, miracle ozzoude wrote:
>
&
Thanks Bruce. resetting means, all my changes will be incorporated into the
final output files?
Best,
Paul
On Thu, Sep 14, 2017 at 3:52 PM, Bruce Fischl
wrote:
> I'm not sure it matters, but if you put it at the end nothing will reset it
>
> On Thu, 14 Sep 2017, miracle
ant the control points to be applied to the aseg? If so, you need
> to also specify -canorm-usecps
>
>
> cheers
> Bruce
> On Thu, 14 Sep 2017, miracle ozzoude wrote:
>
> Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert
>> option for control
rate the aseg? If not, then a). If so, then you
> would just run autorecon2 (instead of autorecon2-cp)
>
> cheers
> Bruce
>
> On Thu, 14 Sep 2017, miracle ozzoude wrote:
>
> I used the expert option for control points and manually edited the
>> aseg.presurf.mgz. Which is
I used the expert option for control points and manually edited the
aseg.presurf.mgz. Which is the proper flag to use in other to incorporate
the respective changes?
a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert
-parallel -openmp 8 -bigventricles -3T -time
or
b) recon-all -a
y something like
>
> mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz
> --segid 77
>
> This will model the strokes as WM hypointensities
>
> On 09/07/2017 11:54 AM, miracle ozzoude wrote:
> > Hello FreeSurfer expert,
> >
> > I have a binar
Hello FreeSurfer expert,
I have a binarized stroke masks of 200 stroke patients that were hand
traced. Since, we have a lot of patients, it will take a lot of time to
edit the aseg.presurf.mgz. The stroke masks were drawn in the native space
and I want to bring them into the freesurfer space, and
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