External Email - Use Caution
What is an offlist?
I am running a longitudinal analysis and in the SUBJECTS directory there are
now the following folders
I had this problem only with subj102 (subj102/mri/orig/102.mgz)
subj001
subj001.long.template18
subj003
t; ha scritto:
>
> Are you sure 102.mgz is from our analysis previously? We typically name the
> volumes 001.mgz, 002.mgz, etc….
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <mailto:freesurfer-boun...@nmr.mgh.harv
quot;
ha scritto:
>Are you sure 102.mgz is from our analysis previously? We typically name
>the volumes 001.mgz, 002.mgz, etc
>
>From: freesurfer-boun...@nmr.mgh.harvard.edu
> On Behalf Of Angela Favaro
>Sent: Sunday, June 28, 2020 1:49 PM
>To: Freesurfer support list
&
; Cheers
> Bruce
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Angela Favaro
> Sent: Sunday, June 28, 2020 8:03 AM
> To: Freesurfer support list
External Email - Use Caution
Dear Freesurfer experts,
I have a problem with a T1 volume of my dataset and I am not able to understand
it.
This volume was correctly analyzed by Freesurfer 6.
Whan I run recon-all with Freesurfer 7.1 the following error appear:
Checking for
it is possible to find a solution
Thank you
Angela
> Il giorno 30 mag 2020, alle ore 12:47, Angela Favaro
> ha scritto:
>
> External Email - Use Caution
>
>
> Dear Freesurfer experts,
> I continued to go on with my data set using 7.1.0 (with a
) and all these subjects were processed without errors using Freesurfer 6.
What do you think is the problem and do you have any suggestion on how to
overcome it?
Thank you
Angela
> Il giorno 28 mag 2020, alle ore 23:18, Angela Favaro
> ha scritto:
>
> External Email -
r/freesurfer/dev/scripts/rca-long-tp-init>
> -o rca-long-tp-init
> sudo chmod +x rca-long-tp-init
>
> Best
> Andrew
>
>
> From: on behalf of Angela Favaro
>
> Reply-To: FS Help
> Date: Wednesday, May 27, 2020 at 4:27 PM
> To: FS Help
> Subje
sues?
Thank you so much!
Angela
> Inizio messaggio inoltrato:
>
> Da: Angela Favaro
> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0
> Data: 23 maggio 2020 10:41:02 CEST
> A: Freesurfer support list
> Rispondi a: Freesurfer support list
>
&
vard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darwin-macOS-7.1.0.tar.gz
> instead.
>
> Best
> Andrew
>
> From: on behalf of Angela
> Favaro
> Reply-To: FS Help
> Date: Sunday, May 24, 2020 at 3:58 AM
> To: FS Help
> Subject: [Freesurfer] hippocampal segmentation f
External Email - Use Caution
Hi all,
I realized that in the MacOS version of freesurfer 7.1.0 there is a file (for
hippocampal segmentation) that is lacking. How can I obtain it?
The file is a Matlab script:
segmentSubjectT1_autoEstimateAlveusML.app
That should be in
External Email - Use Caution
Dear Freesurfer experts,
I am trying to process a dataset with a longitudinal design.
However, after building the template, at the “recon-all -long” command I got
this error:
longmc Done
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
to use
freesurfer 6 only for these 4 subjects?
Or have you any other suggestions?
Thank you for any help
Angela
> Il giorno 15 mag 2020, alle ore 23:26, Angela Favaro
> ha scritto:
>
> External Email - Use Caution
>
>
> Hi doug,
> I tried to re-run
eg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
> /Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220
>
> One factor may be that I'm using CentOS and not Mac. Do you have a linux
> machine you can try it on?
>
>
>
> On 5/15/2020 10:59 AM, Angela Fa
External Email - Use Caution
I have uploaded to you the data using the Martinos Center FileDrop
Hope is a good option for you
Thank you
Angela
> Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro
> ha scritto:
>
> External Email - Use Caution
>
se "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
>
>
> On 5/14/2020 5:03 PM, Angela Favaro wrote:
>> External Email - Use Caution
>>
>> Thank
y supporting lGI anymore, but
> maybe we can get it to work
>
> On 5/13/2020 4:24 PM, Angela Favaro wrote:
>> External Email - Use Caution
>>
>>
>> Hi all,
>> I am using the new version of Freesurfer 7.1.0
>> And I am finding problems
External Email - Use Caution
Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing
The error is after the command find_corresponding_center_FSformat
> linear effect with age (atrophy, linear term is negative= higher age
> with smaller thickness) that slows down at higher ages (quadratic term
> is positive, a floor effect).
>
> Best, Martin
>
> On 04/20/2016 04:50 PM, Angela Favaro wrote:
>> I was finally able to run line
lab don't support the old matlabpool comands any
>> longer. You need to use an older matlab version (less than 8.2.0.29).
>>
>> Best, Martin
>>
>> On 04/05/2016 06:06 PM, Angela Favaro wrote:
>>> Hi Martin, thank you for your help.
>>> I still have pr
tData(M,1,Y,sID); # (sorts the data)
>
>
> Best, Martin
>
>
>
> On 03/20/2016 04:38 PM, Angela Favaro wrote:
>> Dear Freesurfer experts,
>> I need some help with the longitudinal streaming and the use of mixed
>> models in matlab.
>> I followed all the i
;>
>>>> Inviato dal mio dispositivo Huawei
>>>>
>>>> Messaggio originale
>>>> Oggetto: Re: [Freesurfer] eTIV question
>>>> Da: Bruce Fischl
>>>> A: Freesurfer support list
>>>> CC:
>>>>
>>
ative test. I
>> guess you
>> could check the talairach transforms of some of your subjects
>> with eTIVs
>> that don't make sense (or change the most over time) to try to
>> see why
>> this is happening. Or take Mike's suggestion a
orders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO 63110Email: mha...@wustl.edu
>
>
>
>
> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Angela Favaro&q
there is a mistake in the graph, hippocampal volume is TIV2
I apologize for that!
Angela Favaro <angela.fav...@unipd.it> ha scritto:
> Hi Bruce,
> please find attached the graph of the correlation between the two time
> point. I did not find outliers or failures. However
Hi all,
I would be very grateful of any advice for the problem below with e-TIV.
I have another problem with the longitudinal streaming (it is the first
time I use it). I am running the .base and .long procedure in subjects
with only one measure to include them in a mixed liner model analysis (as
Dear Freesurfer experts,
I have a question about eTIV (FS 5.3) which I use as a covariate where
appropriate. Is it in some way influenced by the presence of brain
atrophy?
I have a new sample of subjects in a longitudinal study: at time 1 they
have some atrophy (due to low body weight) that
Hi Bruce
thank you for reassuring me
when pial surface seems a ball of yarn I feel anxious
Angela
> Hi Angela
>
> the images look reasonable - why would you have to discard it?
>
> cheers
> Bruce
> On Tue, 8 Dec
> 2015, angela.fav...@unipd.it wrote:
>
>> Hi Freesurfer experts,
>> I am
Hi all,
for the question below, is it correct this command?
probtrackx2 --network -x /dir/subj001/mask/masks.txt -V 1
--onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 50 --fibthresh=0.01
--distthresh=0.0 --sampvox=0.0 --forcedir --opd -s
/dir/subj001/bedpostX/merged -m
Hi all,
I have a series of volumetric GM masks that I used to calculate a
functional connectivity matrix. Now I want to use the same masks to
calculate a structural connectivity matrix (number of streamlines).
I registered all masks in diffusion space for all subjects.
My idea was to use
Thank you Bruce and MIke!
I was not really looking for something INSTEAD of manual inspection, but
for a measure of the quality of my dataset similarly to what is
reccomended for functional MRI (in that case a SNR below 100 can be
considered a criterion of exclusion).
What are the meaning of these
Hi all,
I am starting to use QAtools in Freesurfer.
The scripts are working well, but I have two problems:
1. the interpretation of output is the first. Are there ranges of
normality for SNR and intensity? Could you please give me some reference
or link about how to interpret these data? Or do I
Thank you!
> Hi Angela
>
> you can load it into matlab with read_curv. If you have the surface and
> the
> tal xform (or transform the surface before loading it into matlab) you can
> find the point on the surface that is closest to a given tal coord and
> read
> out the sulc at that point
>
Hi all,
is there any way (different from manually looking in tksurfer) to know the
value of 'sulc' (or other) in a particular point Talaraich xyz of a
subject?
Thank you!
Angela
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
the following command:
chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: angela favaro
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: angela favaro angela.fav...@unipd.it
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 1, 2015 1:07:31 PM
Subject: Re: [Freesurfer] FS
Hi all,
I have tried to run the new hippocampal segmentation module (after running
the dev version of FS 6. The module did not work and this message error
appears (please find attached the log).
DYLD_LIBRARY_PATH is
/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: angela favaro angela.fav...@unipd.it
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 1, 2015 5:42:07 AM
Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Carolina
personal experience:
usually it is something wrong with the end of paragraph/line
try to delete and re-digit the end of every line
BW
Angela
divHello FS experts,/div
div /div
divI am trying to run qdec. When I load my data table it appears the
following error message:/div
div
THank you Zeke!
Do I have to repeat all the reconall command with the new freesurfer
version or I can use the processed files and run only the hippo
segmentation?
BW
Angela
You can download the dev version of freesurfer which contains the new
hippocampal segmentation from the following page:
Hi Bruce,
I would like to test the beta version of the new hippocampal subfields
segmentation function. Is it at all possible to get it and how?
BW
Angela
yes, but the ones in V6 (which someday will make it out) are more
accurate. You can get a beta and try them out if you want.
cheers
Hi Doug,
thank you for this hint.
I have included --pvr in my mri_glmfit command using a stack of cortical
thickness maps of the same hemisphere (and same subjects in the same
order). I also added a column in my design matrix. It seems to work. Only
when I use the mri_glmfit-sim command, this
Hi all,
I wrote a paper about gyrification in a sample of malnourished patients. I
found only little overlap between maps of significantly rediced cortical
thickness and maps of significantly reduced gyrification index (in
comparison to a group of healthy controls).
One of the reviewer raised the
Hi all, this is really a terrible news!
I am writing a paper using hippocampal subfields (ver 5.3). What is the
problem with segmentation using this tool? Is it reliable at least on some
of the subfield?
When will Freesurfer 6 be released?
Thank you
Angela
Hi Georg,
we will be releasing with
Hi Ruopeng, thank you very much!
Hi Angela,
The issue has been fixed. It is because your annotation has 0's which is
corresponding to black color in the color table). I've made change in my
code so it doesn't display 0's. The fix will be in tomorrow's dev build.
If you are interested in
thank you!
Hi Angela
that actually looks ok. It should follow the gray/white boundary I
believe. Have you looked at it in the individual subject space without
mapping it to the MNI coords? I think there are options in mri_label2vol
to
fill in the whole cortical ribbon instead of just
Hi all,
I have a problem with freeview and I am not sure about the command line to
be used to view a mask.
I have created an annot file and I would like to have a picture of the
mask in the inflated brain with curvature. However when I use the annot
file with tksurfer I am able to do so, but with
Hi Bruce,
I have followed your suggestions using the 'custom fill' botton and then
saving the label and using mri_label2vol. This is the command I used:
mri_label2vol --label gyrif_lh.label --temp MNI152_T1_1mm_brain.nii.gz
--reg $FREESURFER_HOME/average/mni152.register.dat --o gyrif_lh.nii.gz
Dear all,
I found some interesting findings about gyrification and I would like to
test any related problem in structural connectivity.
My idea was to use the area where I found significant lower gyrification
in my sample to perform probabilistic tracking with FSL.
My question is: is there any way
Thank you Bruce!
I have another question:
I would like to show the statistical maps of differences in gyrification
and those of cortical thickness. Is it possible with freeview?
I would also like to calculate the degree of overlapping between these two
maps (percentage of vertices or mm2). Is it
great!
thank you so much
Angela
Sorry, the input should be area, not thickness, ie,
mri_segstats --i $SUBJECTS_DIR/fsaverage/lh.white.avg.area.mgh --seg
gyrbin.mgh --id 1 --sum gyrbin.sum
On 11/2/14 11:30 AM, Douglas Greve wrote:
First, create binary masks, something like (for a
Dear all,
Is there a way to visualize brains in QDEC (or tksurfer or freeview) with
a white background?
thank you for any help
Angela
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
HI all,
I have another problem with mri_glmfit-sim.
It looks for something that is not available in my FS (see below the error
message)
How can I solve this problem?
thank you!
Angela
mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs
--2spaces
cmdline mri_glmfit --y
Hi Doug,
is there a way to perform asymmetry analyses for local gyrification index?
In my xhemi folders there is no LGI surface.
thank you
Angela
You can use --paired-diff-norm instead of --paired-diff, this will compute
(L-R)/((L+R)/2)
You can then divide the output by 2, eg,
fscalc
thank you!
Angela
You can use --paired-diff-norm instead of --paired-diff, this will compute
(L-R)/((L+R)/2)
You can then divide the output by 2, eg,
fscalc output.mgh div 2 -o output.div2.mgh
doug
On 8/24/14 9:52 AM, angela.fav...@unipd.it wrote:
Hi all,
I have a question about
thank you!
that solved my problem!
I think this has something to do with the unix LOCALE because it is
interpreting the 2.0 as 2,0 using the comma , instead of the .
I actually don't know how to fix this. If you run
echo $LANG
does it return
en_US.UTF-8
if not, as a test, try
setenv
Hi all,
I am having a problem with mri_glmfit-sim:
my command was:
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5
--cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this
Hi all,
I have a question about hemispheric asymmetry analyses. The example given
in the wiki shows how to compare lh and rh using a paired t-test. Is it
right?
But how can I calculate (and then compare groups) the laterality index
(L-R)/(L+R)?
Thank you very much for any help
Angela
Hi Doug,
already done!
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5
--cache 2.0 abs
printf: 2.0: not completely converted
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
what does it mean?
I am using a MacOSX 10.6.8
thank you for your help
Angela
Try
Hi Doug,
a further question: my final symmetric atlas seems to be not inflated
enough, but still have important sulcations.
Do I have to perform further iterations (myatlas.i4, myatlas.i5 )
until the resulting volume is good enough? Or which is the correct method
(other than performing
thank you!
sorry, I should have given you a new make_average_volume.
you can get it from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume
On 08/11/2014 07:52 AM, angela.fav...@unipd.it wrote:
Hi Doug, I am having a problem with the last step of
Hi all,
I am running lgi analyses in 5.3 FS version (lion OSX)
one of my subjects failed with a typical message:
lGI for vertex number 39901 of the outer mesh is 1.8067
... remeasuring lGI value for vertex iV = 40001. It may take a few minutes.
WARNING -- Problem for vertex iV = 40001, lGI value
Hi Bruce, hi Maria,
thank you for your suggestions!
However, the message
WARN: time for rh.white is older than rh.inflated
WARN: lh.rh.sphere.reg is empty/missing
WARN: time for lh.white is older than lh.inflated
appears for all subjects I checked.
I tried with the command:
recon-all -s subject
Hi all,
I am now working with the 5.3 version and performing interhemispheric
registration (building my own atlas)
after running for all subjects:
xhemireg --s subj001
surfreg --s subj001 --t fsaverage_sym --lh
surfreg --s subj001 --t fsaverage_sym --xhemi --lh
I have tried first iteration,
Hi Doug, this the command and output (here with only five subjects).
thank you!
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol
--template-only
make_average_surface --out myatlas.i1 --surf-reg
ERROR: Flag --lh unrecognized.
Try adding --lh to the make_average_subject command line. Let me know if
that works and I'll change the docs
doug
On 07/29/2014 05:13 PM, angela.fav...@unipd.it wrote:
Hi Doug, this the command and output (here with only five subjects).
thank you!
I am using 5.3
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol
--template-only --lh
make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004
Hi Doug,
unfortunately the same error message appear... it looks for
rh.fsaverage_sym.sphere.reg
#@# Making rh registration template -
/Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1
mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001
subj001/xhemi
ftp
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
Oh! it works now!
thank you thank you thank you
Angela
when you run make_average_subject, you will still need the --lh
doug
On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote:
ftp
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
Connected to
thank you Marie!
Hi Angela,
Have you tried that:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ?
You can look also in the release notes
(http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using
Matlab 2013.
The issue will be corrected in the
Dear FS experts,
I had no answer to my question below (log was attached in my previous mail)
The error repeated in different subjects and I do not know how to
overcome. Can anyone give me some help?
Angela
Hi all,
I had an error message while running LGI recon
I am using Freesurfer 5.3 with a
Dear Freesurfer team
I am sorry to bore you again with my problems, but I need your help (or
opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my
Freesurfer version (5.0)? Or do I need to use the 5.3 version?
I would prefer
Hi Anthony,
I am not sure I understood what you are saying, but I had no problems with
recon-all commands (I already performed surface, curvature and
gyrification analyses comparing cases and controls, etc...) until I tried
to perform interhemispheric registration.
I had the same problem (see
Hi Doug,
thank you very much!
Angela
I have been able to replicate the error with the patch in 5.1 and I'm
working on a fix.
doug
On 07/07/2014 10:52 AM, angela.fav...@unipd.it wrote:
Dear Freesurfer team
I am sorry to bore you again with my problems, but I need your help (or
opinion)
Hi Adam,
thank you for your mail. I am quite demoralized because I cannot get out
of my problem and I am not receiving support from the mailing list.
Which is, according to you, the solution? Do I need to install 5.3 version
and re-analyse all my subjects from the beginning?
Or do you think that I
Hi all,
I am trying again to perform Surface-based Interhemispheric Registration
in another computer (same version of FS 5.0) and by building my own atlas.
However, there is an error while running xhemireg command (please find the
log attached).
I also noted that the command xhemireg took a lot
Hi Doug
did you see my mail below? any ideas of where the problem could be?
thank you!
I am using the 5.0, but I have followed the instructions and downloaded
the new files as indicated.
the xhemi folder has some folders that are empty (bem, label, src, stats,
tmp), while the others include
sure! thank you
Can you send the log file (or the full terminal output)?
On 06/30/2014 03:11 PM, angela.fav...@unipd.it wrote:
Hi all,
I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command:
'surfreg --s
Hi all,
I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command:
'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below
(indeed in the xhemi/label directory, there is no file)
What can I do?
Hi all,
I would need some information about the local gyrification index.
I run the analyses and found which are the average indices for subject and
hemisphere.
1. Is there a method to perform vertex-wise group statistics? that is may
I compare maps of gyrification across groups?
2. Is there a
Hi all,
I found answers to ponts 1 and 2 in the webpage.
Sorry for my question
Angela
Hi all,
I would need some information about the local gyrification index.
I run the analyses and found which are the average indices for subject and
hemisphere.
1. Is there a method to perform
to restrict the area of a vertex-analysis to my ROI (visual brain
areas)
2. When performing a vertex-analysis, is it correct to include TIV (total
intracranial volume) as a nuisance variable?
Thank you for any help
Angela
Angela Favaro, MD, PhD
Psychiatric Clinic
Department of Neurosciences
via
--in
rh.thickness.fsaverage.mgh --sum segstats-mask21.txt
give:
ERROR: dimension mismatch between input volume and seg
input 27307 1 6
seg 23406 1 7
What can I do to solve this problem?
Thank you for your help!
Angela
Angela Favaro, MD, PhD, MSc
Psychiatric Clinic
Department
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