Re: [Freesurfer] Putting results from probabilistic tractography on the surface

[Bruce Fischl]

Hi Sara

no worries. The units are mm, and use -avg averages the values and max 
takes the max over them (which is a somewhat dicey thing to do if you are 
going to do stats afterwards).


cheers
Bruce

On Wed, 11 Jul 2018, Sims, Sara A wrote:


   External Email - Use Caution

Bruce,
The help file and wiki don't explain the units of the min, max, and del. I 
still can't get the data to sample onto the surface correctly and so I'm 
wondering if it has something to do with my assumptions about how this command 
flag is working. What unit are these values supposed to be in?
Also is the difference between projdist-avg and projdist-max that avg averages 
all values (including zeros) and max finds the highest value from the points 
between min and max?
Sorry to get into the nitty gritty, I am just trying to understand all the 
options so I can use them appropriately.

Thanks,
Sara Sims

On 7/9/18, 3:15 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

   I think it is short for "delta" - how far about the samples are

   On Mon, 9
   Jul 2018, Sims, Sara A wrote:

   >External Email - Use Caution
   >
   > Bruce,
   > What does "del" mean in the --projdist-avg flag?
   >
   > Sara Sims
   > Graduate Research Fellow
   > University of Alabama at Birmingham
   > Department of Psychology
   > 205-975-4060
   > sno...@uab.edu
   >
   > On 6/26/18, 2:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:
   >
   >Hi Sara
   >check out the help (with --help). For example you could use:
   >
   >--projdist-avg min max del : average along normal
   >
   >cheers
   >Bruce
   >On Tue, 26 Jun
   >2018, Sims, Sara A wrote:
   >
   >>External Email - Use Caution
   >>
   >> Bruce,
   >> Thanks! So if I set it to say 4mm would it sample from 0-4mm or just 
from exactly 4mm and ignore things slightly closer to the surface?
   >> My problem would be somethings could be 2mm or 3mm etc. and it's not 
exactly the same all the way around the brain.
   >>
   >> Sara Sims
   >> Graduate Research Fellow
   >> University of Alabama at Birmingham
   >> Department of Psychology
   >> 205-975-4060
   >> sno...@uab.edu
   >>
   >> On 6/26/18, 2:27 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  
wrote:
   >>
   >>Hi Sara
   >>
   >>you can use a negative projdist in mri_vol2surf
   >>
   >>cheers
   >>Bruce
   >>On Tue, 26 Jun 2018, Sims,
   >>Sara A wrote:
   >>
   >>>
   >>> External Email - Use Caution
   >>>
   >>> Hello,
   >>>
   >>> I have outputs from FSL probtrackx that I would like to display 
on Freesurfer surfaces. If I
   >>> put the volume into freesurfer space how can I get it to sample 
onto a surface when the
   >>> values are in white matter and not grey matter? To rephrase, how 
can I pull data from white
   >>> matter (just below the grey matter) and display it on a surface?
   >>>
   >>>
   >>>
   >>> Many thanks,
   >>>
   >>> Sara
   >>>
   >>>
   >>>
   >>
   >>
   >> ___
   >> Freesurfer mailing list
   >> Freesurfer@nmr.mgh.harvard.edu
   >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
   >>
   >>
   >>
   >
   >
   > ___
   > Freesurfer mailing list
   > Freesurfer@nmr.mgh.harvard.edu
   > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
   >
   >
   >


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Re: [Freesurfer] Custom color map in Freeview

[Bruce Fischl]

there is some code around to display each parcel with a different value, 
but I'm not sure exactly what it is. YOu could certainly do it in matlab

if you wanted to (use read_annotation.m to read in the .annot file)

Cheers
Bruce

On Wed, 11 Jul 2018, Ben Smith wrote:



External Email - Use Caution

Hi Bruce,
Some background: 

I have already extracted ROI timeseries using the following method:
 *  use mri_vol2vol to transform the functional images to structural space (yes 
these were very
large images; I did it one at a time)
 *  use mri_segstats to segment the image into cortical parcellations and 
subcortical segmentations
That gave me raw timecourses for each segment and parcellation. I used my own 
code to mean-center
and high-pass filter (specificaly, linear, quadratic, and cubic regressors); 
then applied an HRF
function. I was then able to extract a single activity value for each ROI and 
each event in my
design.
So for each subject I now have an N*M matrix where N is the number of events 
and M is the number of
ROIs, representing mean activity in each ROI during each event.
I'm then estimating the covariance of activity in these ROIs with reward 
prediction error according
to an RL model.
---

So back to freesurfer - I have a single covariance value for each ROI and I 
want to show that
covariance in an illustration, where each ROI is color-coded according to its 
covariance value.

It's good to know the annotations (e.g., label/rh.aparc.a2009s.annot, right?) 
are what I need for
this, but they're not plain text, so I don't know how to use them to create a 
colormap like Ruopeng
suggested.





___
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
p | +1 323-385 9349
skype | ben.smith.nz



On Tue, Jul 10, 2018 at 5:54 PM Bruce Fischl  wrote:
  Hi Ben

  can you explain a bit more explicitly what you are trying to do? The
  annotations are exactly what you suggest (a parcellation ID for every
  vertex)

  cheers
  Bruce
  On Tue, 10 Jul 2018, Ben Smith wrote:

  >
  > External Email - Use Caution
  >
  > Got it, thanks!
  > Could you tell me how I can map a particular ROI (for instance the 
Destrieux cortical
  surface ROIs)
  > to a set of vertices that make up the ROI? Is there a lookup table I 
can use?
  > ___
  > Ben Smith, MSc.
  > Ph.D. Candidate
  > University of Southern California
  > https://bjsmith.github.io/
  > p | +1 323-385 9349
  > skype | ben.smith.nz
  >
  >
  >
  > On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang 
 wrote:
  >
  >       Hi Ben,
  >
  >       My last email was referring to how to load custom color map for 
volume viewing.
  If you
  >       want to load custom color for surface, you need to create and 
load an RGB map
  file. The
  >       file can be a text file contains N lines of RGB color like this:
  >
  >       R1, G1, B1
  >       R2, G2, B2
  >
  >       ...
  >
  >       or a volume file with dimension of  N x 3 x1. N must match the 
number of
  vertices of the
  >       surface.
  >
  >       Best,
  >       Ruopeng
  >
  >
  >       On 07/10/2018 04:57 PM, Ben Smith wrote:
  >
  >       External Email - Use Caution
  >
  >       I've been trying to do this as well, but I can't see the right 
place to specify
  in
  >       freesurfer to specify an alternative lookup table.
  > For instance, if I am coloring a pial surface, then the first 
possibility is to set a
  > Color (where I can "load RGB map"). But I get an error "Cannot load 
RGB" file if I try
  > to use that to load an LUT format file. The other option is where it says 
"heatmap" i
  > can change the option to select a custom label, but if I try to enter 
an LUT file into
  > there, freeview crashes (which is fine, I guess that was the wrong 
place).
  >
  > So can anyone tell me what I'm missing for the place to load the LUT 
file or an
  > alternative colormap?
  >
  > Thanks for your help!
  >
  > Regards
  >
  > Ben
  >
  > On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang 
 wrote:
  >
  >       It looks like a customized look up table will work for your case. 
You can
  >       simply select "Lookup table" as the colormap and load your own 
lookup table.
  >       To create your own look up table, you can refer to the content of
  >       FreeSurferColorLUT.txt file in your freesurfer installation 
directory.
  >
  >       Best,
  >       Ruopeng
  >
  >       On 03/27/2018 03:59 PM, Anna Mynick wrote:
  >       Hi all, 
  > I’m wondering whether there’s a way to create a custom color map in 
Freeview
  > that would operate as a 

Re: [Freesurfer] Putting results from probabilistic tractography on the surface

[Sims, Sara A]

External Email - Use Caution

Bruce,
The help file and wiki don't explain the units of the min, max, and del. I 
still can't get the data to sample onto the surface correctly and so I'm 
wondering if it has something to do with my assumptions about how this command 
flag is working. What unit are these values supposed to be in?
Also is the difference between projdist-avg and projdist-max that avg averages 
all values (including zeros) and max finds the highest value from the points 
between min and max?
Sorry to get into the nitty gritty, I am just trying to understand all the 
options so I can use them appropriately. 

Thanks,
Sara Sims 

On 7/9/18, 3:15 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl"  wrote:

I think it is short for "delta" - how far about the samples are

On Mon, 9 
Jul 2018, Sims, Sara A wrote:

>External Email - Use Caution
>
> Bruce,
> What does "del" mean in the --projdist-avg flag?
>
> Sara Sims
> Graduate Research Fellow
> University of Alabama at Birmingham
> Department of Psychology
> 205-975-4060
> sno...@uab.edu
>
> On 6/26/18, 2:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:
>
>Hi Sara
>check out the help (with --help). For example you could use:
>
>--projdist-avg min max del : average along normal
>
>cheers
>Bruce
>On Tue, 26 Jun
>2018, Sims, Sara A wrote:
>
>>External Email - Use Caution
>>
>> Bruce,
>> Thanks! So if I set it to say 4mm would it sample from 0-4mm or just 
from exactly 4mm and ignore things slightly closer to the surface?
>> My problem would be somethings could be 2mm or 3mm etc. and it's not 
exactly the same all the way around the brain.
>>
>> Sara Sims
>> Graduate Research Fellow
>> University of Alabama at Birmingham
>> Department of Psychology
>> 205-975-4060
>> sno...@uab.edu
>>
>> On 6/26/18, 2:27 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Bruce Fischl"  wrote:
>>
>>Hi Sara
>>
>>you can use a negative projdist in mri_vol2surf
>>
>>cheers
>>Bruce
>>On Tue, 26 Jun 2018, Sims,
>>Sara A wrote:
>>
>>>
>>> External Email - Use Caution
>>>
>>> Hello,
>>>
>>> I have outputs from FSL probtrackx that I would like to display 
on Freesurfer surfaces. If I
>>> put the volume into freesurfer space how can I get it to sample 
onto a surface when the
>>> values are in white matter and not grey matter? To rephrase, 
how can I pull data from white
>>> matter (just below the grey matter) and display it on a surface?
>>>
>>>
>>>
>>> Many thanks,
>>>
>>> Sara
>>>
>>>
>>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Custom color map in Freeview

[Ben Smith]

External Email - Use Caution

Hi Bruce,

Some background:

I have already extracted ROI timeseries using the following method:

   - use mri_vol2vol to transform the functional images to structural space
   (yes these were very large images; I did it one at a time)
   - use mri_segstats to segment the image into cortical parcellations and
   subcortical segmentations

That gave me raw timecourses for each segment and parcellation. I used my
own code to mean-center and high-pass filter (specificaly, linear,
quadratic, and cubic regressors); then applied an HRF function. I was then
able to extract a single activity value for each ROI and each event in my
design.
So for each subject I now have an N*M matrix where N is the number of
events and M is the number of ROIs, representing mean activity in each ROI
during each event.
I'm then estimating the covariance of activity in these ROIs with reward
prediction error according to an RL model.
---

So back to freesurfer - I have a single covariance value for each ROI and I
want to show that covariance in an illustration, where each ROI is
color-coded according to its covariance value.

It's good to know the annotations (e.g., label/rh.aparc.a2009s.annot,
right?) are what I need for this, but they're not plain text, so I don't
know how to use them to create a colormap like Ruopeng suggested.





___
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
p | +1 323-385 9349
skype | ben.smith.nz



On Tue, Jul 10, 2018 at 5:54 PM Bruce Fischl 
wrote:

> Hi Ben
>
> can you explain a bit more explicitly what you are trying to do? The
> annotations are exactly what you suggest (a parcellation ID for every
> vertex)
>
> cheers
> Bruce
> On Tue, 10 Jul 2018, Ben Smith wrote:
>
> >
> > External Email - Use Caution
> >
> > Got it, thanks!
> > Could you tell me how I can map a particular ROI (for instance the
> Destrieux cortical surface ROIs)
> > to a set of vertices that make up the ROI? Is there a lookup table I can
> use?
> > ___
> > Ben Smith, MSc.
> > Ph.D. Candidate
> > University of Southern California
> > https://bjsmith.github.io/
> > p | +1 323-385 9349
> > skype | ben.smith.nz
> >
> >
> >
> > On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang 
> wrote:
> >
> >   Hi Ben,
> >
> >   My last email was referring to how to load custom color map for
> volume viewing. If you
> >   want to load custom color for surface, you need to create and load
> an RGB map file. The
> >   file can be a text file contains N lines of RGB color like this:
> >
> >   R1, G1, B1
> >   R2, G2, B2
> >
> >   ...
> >
> >   or a volume file with dimension of  N x 3 x1. N must match the
> number of vertices of the
> >   surface.
> >
> >   Best,
> >   Ruopeng
> >
> >
> >   On 07/10/2018 04:57 PM, Ben Smith wrote:
> >
> >   External Email - Use Caution
> >
> >   I've been trying to do this as well, but I can't see the right
> place to specify in
> >   freesurfer to specify an alternative lookup table.
> > For instance, if I am coloring a pial surface, then the first
> possibility is to set a
> > Color (where I can "load RGB map"). But I get an error "Cannot load RGB"
> file if I try
> > to use that to load an LUT format file. The other option is where it
> says "heatmap" i
> > can change the option to select a custom label, but if I try to enter an
> LUT file into
> > there, freeview crashes (which is fine, I guess that was the wrong
> place).
> >
> > So can anyone tell me what I'm missing for the place to load the LUT
> file or an
> > alternative colormap?
> >
> > Thanks for your help!
> >
> > Regards
> >
> > Ben
> >
> > On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang 
> wrote:
> >
> >   It looks like a customized look up table will work for your case.
> You can
> >   simply select "Lookup table" as the colormap and load your own
> lookup table.
> >   To create your own look up table, you can refer to the content of
> >   FreeSurferColorLUT.txt file in your freesurfer installation
> directory.
> >
> >   Best,
> >   Ruopeng
> >
> >   On 03/27/2018 03:59 PM, Anna Mynick wrote:
> >   Hi all,
> > I’m wondering whether there’s a way to create a custom color map in
> Freeview
> > that would operate as a alternative to the preset Greyscale, Heatmap,
> NIH,
> > PET, Jet and GE Color options.
> >
> > Ideally, I could assign each number value a given color, e.g. every “0”
> > value in an .nii file is black, every “1” value is red, every “2” value
> is
> > blue, every “3" is green and so on. I already have the RGB values worked
> out
> > for each number value; I just need to know how to format this information
> > and where to put it so that I can my custom colormap as an option in
> > Freeview.
> >
> > For my purposes, there would be no need to adjust the assigned colors
> based
> > on the overall range of 

[Freesurfer] make_average_subject error

[Wang, Xiaoyu]

External Email - Use Caution

Hello FreeSurfer Developers,

I am attempting to perform group analysis on a group of subjects. However, When 
I am trying to create an average subject I get the following error.

mghRead(mri/norm.mgz, -1) could not open file

I went into the average folder but I could not find norm.mgz anywhere.
Looking further up on the log, it would seem that norm.mgz is supposed to be 
relabled from aseg.presurf.hypos

However, said file is still there.

I have looked in the wiki and found a few others who have had similar issues to 
me however, I can't see the solution or a reply. Does anyone have any Idea what 
I'm doing wrong?

I have attached the recon-all.error as well as the recon-all log if it will be 
of any help

Sincerely

Xiaoyu Wang


recon-all.error
Description: recon-all.error


recon-all.log
Description: recon-all.log
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Re: [Freesurfer] Correct for sulcuses & ventricles size

[Bruce Fischl]

I suppose you could look for voxels that outside of the cortex and 
adjacent to it

On Wed, 11 Jul 2018, John Anderson wrote:



External Email - Use Caution

Dear Dr Bruce,

Thank you for the response. Indeed, I was completely wrong, these represent a 
pathology and should
not correct for!

Kindly, I have one additional question not relevant to the subject of this 
email. Is there any way
in Freesurfer to create mask for the regions between the sulcuses. I want to 
compute PET signal in
these regions and normalize for it.

Thank you so much!
John

Hi John

 

why do you want to correct for them? They likely represent a pathological 
process, so correcting for
them may remove whatever effects you are looking for, no? The space between the 
sulci and the
ventricle volume won't directly affect surface-based analysis, but of course 
the sulcal widening
likely reflects cortical atrophy that will be

 cheers

Bruce




‐‐‐ Original Message ‐‐‐
On July 11, 2018 11:37 AM, John Anderson  wrote:

  Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have 
different degrees of
atrophy. Looking into the individual scans, the subjects are largely different 
in the space
between the sulcuses and the size of ventricles. My questions are:
1. Is there any way to correct for these differences in the surface based 
analysis?
2. Including eTIV covariate does it help in this case?
3. Does the resampling to "fsaverage" overcome the challenge of these 
differences between the
subjects? 

I appreciate any advice,
John



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Re: [Freesurfer] Correct for sulcuses & ventricles size

[John Anderson]

External Email - Use Caution

Dear Dr Bruce,

Thank you for the response. Indeed, I was completely wrong, these represent a 
pathology and should not correct for!

Kindly, I have one additional question not relevant to the subject of this 
email. Is there any way in Freesurfer to create mask for the regions between 
the sulcuses. I want to compute PET signal in these regions and normalize for 
it.

Thank you so much!
John

Hi John

why do you want to correct for them? They likely represent a pathological 
process, so correcting for them may remove whatever effects you are looking 
for, no? The space between the sulci and the ventricle volume won't directly 
affect surface-based analysis, but of course the sulcal widening likely 
reflects cortical atrophy that will be

 cheers

Bruce

‐‐‐ Original Message ‐‐‐
On July 11, 2018 11:37 AM, John Anderson  wrote:

> Dear Freesurfer experts,
> I have two groups of subjects (healthy and patients). The patients have 
> different degrees of atrophy. Looking into the individual scans, the subjects 
> are largely different in the space between the sulcuses and the size of 
> ventricles. My questions are:
> 1. Is there any way to correct for these differences in the surface based 
> analysis?
> 2. Including eTIV covariate does it help in this case?
> 3. Does the resampling to "fsaverage" overcome the challenge of these 
> differences between the subjects?
>
> I appreciate any advice,
> John___
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[Freesurfer] Cortical Thickness at Individual Vertices

[James Gullickson]

External Email - Use Caution

All,

I am comparing cortical thickness between subjects with and without mild
traumatic brain injury (mTBI). So far the contrasts in QDEC have not been
significant after correcting for multiple comparisons. I am not necessarily
surprised at this due to the heterogeneous nature of mTBI in our sample,
i.e. we do not expect any two subjects to have damage in the same area. I
am interested in ways to compare cortical thickness that are not dependent
on a single ROI having an effect across subjects. One way I have tried is
calculating z-scores for the values in the aparc.stats file, and using the
number of abnormally low ROIs as a dependant variable to compare between
groups.

Is there a way to look at thickness differences at an even more general
level? E.g. by comparing the number of vertices with abnormally low
thickness? If so how would one go about that with Freesurfer data?

This paper takes a similar approach with DTI. I'd like to do something
analogous to their "number of voxels with low FA" analysis.
https://www.sciencedirect.com/science/article/pii/S1053811911012146

Thanks,

James
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Re: [Freesurfer] Errors preprocess

[Lee, Seonjoo]

External Email - Use Caution

This works! Thank you so much for your help.
-Seonjoo

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Boyd, Emma
Sent: Wednesday, July 11, 2018 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Errors preprocess


Hi Seonjoo,



What directory are you in when you run preproc-sess? You should run this 
command from the data/ dir.



Emma





-

Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Lee, Seonjoo 
mailto:sl3...@cumc.columbia.edu>>
Sent: Wednesday, July 11, 2018 8:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors preprocess


External Email - Use Caution

Dear Freesurfer experts,

I tried to run preproc-sess but did not have much luck to make it work.



I converted resting fmri file into .nii, and I created the following directory 
structure and it's stored under /data/sub1/rest/001/fMRI.nii:





/data

/data/sub1

/data/sub1/rest

/data/sub1/rest/001/

/data/sub1/rest/001/fMRI.nii





Then I ran



preproc-sess -s sub1 -fsd rest -surface $FSAVERAGE_DIR/fsaverage lhrh -mni305 
-fwhm 5 -per-run



And I kept getting the following error message:



ERROR: cound not find session sub1



To run freesurfer I specified SUBEJCTS_DIR as /data (I don't think it matters, 
though...)





export FREESURFER_HOME=/Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh

SUBJECTS_DIR=/data



Any suggestion to make it work?

Thanks.

-Seonjoo












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Re: [Freesurfer] Regenerate Qcache without Recon-ALL

[Mr. Tass]

External Email - Use Caution

jesus almost panicked there
haha
cheers mate


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Wednesday, July 11, 2018 4:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Regenerate Qcache without Recon-ALL

no, you can just run with -qcache for each subject. Don't include -all or
-autorecon2 or anthing, just subject id and -qcache. It should be fast
On Wed, 11 Jul 2018,
Mr. Tass wrote:

>
> External Email - Use Caution
>
> Hello
>
> just a quick question
> i didn't run recon-all using the -qcache
> do i have to start all over ?  the initial run took a week
>
> Please advise if there is a way to fix that without having to restart 
> recon-all again
>
>
> thank you
>
>
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[Freesurfer] mris_ca_label seed

[Rosemary Nicholas]

External Email - Use Caution

Hello,

I am running a dataset through version 6.0 of Freesurfer on Linux,
extracting results for both the Desikan atlas and our own atlas.  When
extracting the stats for our atlas, the results were varying considerably
(sometimes up to 10%) in test-retest runs.

The release notes for 4.5 indicate that the default setting for
mris_ca_label should use the same number as a seed, and therefore give the
same results, but it doesn't.

"The binaries in the recon-all stream which are subject to variability due
to usage of a random number generator (mris_smooth, mris_sphere,
mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with
the same number, with the result being that repeated runs of the recon-all
stream on a subject on the same platform will always give identical
results."

The issue seems to be resolved by adding -seed 1234 as a flag to
mris_ca_label.

I would like to understand what this is actually doing though, before
applying it to all my data.  What is the random number generator used for?
What does setting it to 1234 actually do?  It isn't listed in the optional
flagged arguments. Is it just deciding which vertex is labeled first?

Here is how we are running it (in two independent scripts):

FIRST:

# autorecon1 including data conversion
recon-all -i $mprage/001 -autorecon1 -subjid $s

# autorecon2 with threshold adjustments
recon-all -seg-wlo 60 -seg-ghi 70 -autorecon2 -subjid $s

# autorecon3
recon-all -autorecon3 -subjid $s

THEN:

mris_ca_label $s $h sphere.reg
/g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot

modified to:
mris_ca_label -seed 1234 $s $h sphere.reg
/g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot



Thank you,

Rosemary Nicholas
Center for Neurodevelopmental and Imaging Research
Kennedy Krieger Institute
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Re: [Freesurfer] Regenerate Qcache without Recon-ALL

[Bruce Fischl]

no, you can just run with -qcache for each subject. Don't include -all or 
-autorecon2 or anthing, just subject id and -qcache. It should be fast
On Wed, 11 Jul 2018, 
Mr. Tass wrote:




External Email - Use Caution

Hello

just a quick question
i didn't run recon-all using the -qcache
do i have to start all over ?  the initial run took a week

Please advise if there is a way to fix that without having to restart recon-all 
again


thank you

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[Freesurfer] Regenerate Qcache without Recon-ALL

[Mr. Tass]

External Email - Use Caution

Hello

just a quick question
i didn't run recon-all using the -qcache
do i have to start all over ?  the initial run took a week

Please advise if there is a way to fix that without having to restart recon-all 
again


thank you
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

[Jasmin Alves]

External Email - Use Caution

And yes, pwd and dirname are both in my path.

m-100205:bin PageLab$ pwd

/Users/PageLab/Documents/freesurfer/bin

m-100205:bin PageLab$ dirname

usage: dirname path

m-100205:bin PageLab$ dirname path

.



On Wed, Jul 11, 2018 at 9:25 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Sorry, I meant pwd, dirname, etc
>
>
>
> --
>
> 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.uk/
>
>
>
>
>
> *From: * on behalf of Jasmin
> Alves 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 11 July 2018 at 17:16
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh:
> Command not found.
>
>
>
> *External Email - Use Caution*
>
> Hello Eugenio,
>
>
>
> Thank you for the reply. The script, segmentSF_T1.sh is found in
>
> /Users/PageLab/Documents/freesurfer/bin
>
>
>
>
>
>
>
> The freesurfer environment has been set to
>
> /Users/PageLab/Documents/freesurfer
>
>
>
>
>
> So, I am not sure why the script is inaccessible. Recon-all works great.
>
>
>
> Thanks,
> Jasmin
>
> On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> *External Email - Use Caution*
>
> Dear Jasmin,
>
> The script segmentSF_T1.sh does not seem to be able to find basic commands
> like pwd and dirname. Are these in your path?
>
> 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.uk/
> 
>
>
>
>
>
> *From: * on behalf of Jasmin
> Alves 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 11 July 2018 at 16:26
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh:
> Command not found.
>
>
>
> *External Email - Use Caution*
>
> Hello FreeSurfer Developers,
>
>
>
> I am trying to analyze the subfields of the hippocampus using FreeSurfer
> 6.0 based on the tutorial, "Segmentation of hippocampal subfields".
> However, several errors come up when I run:
>
> recon-all -s 102 -hippocampal-subfields-T1
>
>
>
> #@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18
> PDT 2018
>
> dirname: Command not found.
>
> pwd: Command not found.
>
> pwd: Command not found.
>
> /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
>
> #
>
> #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18
> PDT 2018
>
> dirname: Command not found.
>
> pwd: Command not found.
>
> pwd: Command not found.
>
> /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
>
>
>
> I have searched through the list to see if anyone else has had this issue
> but to no avail.
>
>
>
> Version:
>
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>
>
>
> OS: X V 10.9.5
>
>
>
> Thanks!
>
> Jasmin
>
>
>
>
> --
>
> Jasmin Alves
>
> Doctoral Candidate
>
> Medical Biology Graduate Program
>
> University of Southern California
>
> jal...@usc.edu
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.
> nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=
> clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=
> w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8=JWFtZN0TxhbF-
> szDNVVAGtRlTVerKBV7GCF0cFlu-_w=
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
> partners.org_complianceline=DwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN
> 0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=w4MGsgIqoYbSnHHZCr8GnKo65Vd50P
> dt3Ha1YYG4Rw8=2mrR0Thpt73B1ran6vJjkbnFjoZ7wovDcNc23JUxZLY= . If the
> e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
>
>
> --
>
> Jasmin Alves
>
> Doctoral Candidate
>
> Medical Biology Graduate Program
>
> University of Southern California
>
> 

Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

[Jasmin Alves]

External Email - Use Caution

Hello Eugenio,

I noticed Matlab doesn't open when I run the hippocampal analysis, so when
I tried to click on the file, segmentSubjectT1_autoEstimateAlveusML,

I encountered the following error:

Check with the developer to make sure segmentSubjectT1_autoEstimateAlveusML
works with this version of OS X. You may need to reinstall the application.
Be sure to install any available updates for the application and OS X.

Thanks,
Jasmin

On Wed, Jul 11, 2018 at 9:15 AM, Jasmin Alves  wrote:

> Hello Eugenio,
>
> Thank you for the reply. The script, segmentSF_T1.sh is found in
>
> /Users/PageLab/Documents/freesurfer/bin
>
>
>
>
> The freesurfer environment has been set to
>
> /Users/PageLab/Documents/freesurfer
>
>
> So, I am not sure why the script is inaccessible. Recon-all works great.
>
> Thanks,
> Jasmin
> On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
>> External Email - Use Caution
>>
>> Dear Jasmin,
>>
>> The script segmentSF_T1.sh does not seem to be able to find basic
>> commands like pwd and dirname. Are these in your path?
>>
>> 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.uk/
>>
>>
>>
>>
>>
>> *From: * on behalf of Jasmin
>> Alves 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Wednesday, 11 July 2018 at 16:26
>> *To: *Freesurfer support list 
>> *Subject: *[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh:
>> Command not found.
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hello FreeSurfer Developers,
>>
>>
>>
>> I am trying to analyze the subfields of the hippocampus using FreeSurfer
>> 6.0 based on the tutorial, "Segmentation of hippocampal subfields".
>> However, several errors come up when I run:
>>
>> recon-all -s 102 -hippocampal-subfields-T1
>>
>>
>>
>> #@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18
>> PDT 2018
>>
>> dirname: Command not found.
>>
>> pwd: Command not found.
>>
>> pwd: Command not found.
>>
>> /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
>>
>> #
>>
>> #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18
>> PDT 2018
>>
>> dirname: Command not found.
>>
>> pwd: Command not found.
>>
>> pwd: Command not found.
>>
>> /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
>>
>>
>>
>> I have searched through the list to see if anyone else has had this issue
>> but to no avail.
>>
>>
>>
>> Version:
>>
>> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>>
>>
>>
>> OS: X V 10.9.5
>>
>>
>>
>> Thanks!
>>
>> Jasmin
>>
>>
>>
>>
>> --
>>
>> Jasmin Alves
>>
>> Doctoral Candidate
>>
>> Medical Biology Graduate Program
>>
>> University of Southern California
>>
>> jal...@usc.edu
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm
>> r.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=clK
>> 7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rN
>> RHLug=w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8=
>> JWFtZN0TxhbF-szDNVVAGtRlTVerKBV7GCF0cFlu-_w=
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part
>> ners.org_complianceline=DwIBAg=clK7kQUTWtAVEOVIgvi0NU5BO
>> UHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=w4MGsgIqoYbSnH
>> HZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8=2mrR0Thpt73B1ran6vJjkbnFjoZ7
>> wovDcNc23JUxZLY= . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> Jasmin Alves
> Doctoral Candidate
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu
>
>


-- 
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Sorry, I meant pwd, dirname, etc

--
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.uk/


From:  on behalf of Jasmin Alves 

Reply-To: Freesurfer support list 
Date: Wednesday, 11 July 2018 at 17:16
To: Freesurfer support list 
Subject: Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: 
Command not found.


External Email - Use Caution
Hello Eugenio,

Thank you for the reply. The script, segmentSF_T1.sh is found in

/Users/PageLab/Documents/freesurfer/bin




The freesurfer environment has been set to

/Users/PageLab/Documents/freesurfer


So, I am not sure why the script is inaccessible. Recon-all works great.

Thanks,
Jasmin
On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution
Dear Jasmin,
The script segmentSF_T1.sh does not seem to be able to find basic commands like 
pwd and dirname. Are these in your path?
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.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Jasmin Alves mailto:jal...@usc.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, 11 July 2018 at 16:26
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command 
not found.


External Email - Use Caution
Hello FreeSurfer Developers,

I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 
based on the tutorial, "Segmentation of hippocampal subfields".
However, several errors come up when I run:

recon-all -s 102 -hippocampal-subfields-T1

#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 
2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

I have searched through the list to see if anyone else has had this issue but 
to no avail.

Version:

freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

OS: X V 10.9.5

Thanks!
Jasmin


--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu


___
Freesurfer mailing list
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https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8=JWFtZN0TxhbF-szDNVVAGtRlTVerKBV7GCF0cFlu-_w=


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=DwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8=2mrR0Thpt73B1ran6vJjkbnFjoZ7wovDcNc23JUxZLY=
 . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu

___
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Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

[Jasmin Alves]

External Email - Use Caution

Hello Eugenio,

Thank you for the reply. The script, segmentSF_T1.sh is found in

/Users/PageLab/Documents/freesurfer/bin




The freesurfer environment has been set to

/Users/PageLab/Documents/freesurfer


So, I am not sure why the script is inaccessible. Recon-all works great.

Thanks,
Jasmin
On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Dear Jasmin,
>
> The script segmentSF_T1.sh does not seem to be able to find basic commands
> like pwd and dirname. Are these in your path?
>
> 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.uk/
>
>
>
>
>
> *From: * on behalf of Jasmin
> Alves 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 11 July 2018 at 16:26
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh:
> Command not found.
>
>
>
> *External Email - Use Caution*
>
> Hello FreeSurfer Developers,
>
>
>
> I am trying to analyze the subfields of the hippocampus using FreeSurfer
> 6.0 based on the tutorial, "Segmentation of hippocampal subfields".
> However, several errors come up when I run:
>
> recon-all -s 102 -hippocampal-subfields-T1
>
>
>
> #@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18
> PDT 2018
>
> dirname: Command not found.
>
> pwd: Command not found.
>
> pwd: Command not found.
>
> /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
>
> #
>
> #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18
> PDT 2018
>
> dirname: Command not found.
>
> pwd: Command not found.
>
> pwd: Command not found.
>
> /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
>
>
>
> I have searched through the list to see if anyone else has had this issue
> but to no avail.
>
>
>
> Version:
>
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>
>
>
> OS: X V 10.9.5
>
>
>
> Thanks!
>
> Jasmin
>
>
>
>
> --
>
> Jasmin Alves
>
> Doctoral Candidate
>
> Medical Biology Graduate Program
>
> University of Southern California
>
> jal...@usc.edu
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=
> clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=
> w4MGsgIqoYbSnHHZCr8GnKo65Vd50Pdt3Ha1YYG4Rw8=JWFtZN0TxhbF-
> szDNVVAGtRlTVerKBV7GCF0cFlu-_w=
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
> partners.org_complianceline=DwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN
> 0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=w4MGsgIqoYbSnHHZCr8GnKo65Vd50P
> dt3Ha1YYG4Rw8=2mrR0Thpt73B1ran6vJjkbnFjoZ7wovDcNc23JUxZLY= . If the
> e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Jasmin,
The script segmentSF_T1.sh does not seem to be able to find basic commands like 
pwd and dirname. Are these in your path?
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.uk/


From:  on behalf of Jasmin Alves 

Reply-To: Freesurfer support list 
Date: Wednesday, 11 July 2018 at 16:26
To: Freesurfer support list 
Subject: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command 
not found.


External Email - Use Caution
Hello FreeSurfer Developers,

I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 
based on the tutorial, "Segmentation of hippocampal subfields".
However, several errors come up when I run:

recon-all -s 102 -hippocampal-subfields-T1

#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 
2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

I have searched through the list to see if anyone else has had this issue but 
to no avail.

Version:

freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

OS: X V 10.9.5

Thanks!
Jasmin


--
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu

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[Freesurfer] ERROR: Transform file should be eddy_correct/eddy log file or .mat file

[Renew Andrade]

External Email - Use Caution

Hello:
I have a problem when running trac-all preprocessing. I have X11 and FSL 
installed. Not Matlab I don’t know if I need it I think only for fMRI. 
Sincerely,
Andrade. 

Renes-MacBook-Air-2:diffusion_tutorial andraderenew$ trac-all -prep -c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons
INFO: Diffusion root is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /usr/local/freesurfer/dev
trac-preproc -c 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local
 -log 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log
 -cmd 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd
#-
/Applications/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Wed Jul 11 17:53:23 CEST 2018
mri_convert --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No 
INFO: Found 75 files in 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory 
INFO: found 70 files in series
INFO: loading series header info.

RunNo = 10
WARNING: Run 1 appears to be truncated
  Files Found: 70, Files Expected (lRep+1): 120
FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 
ScannerModel  Trio
PatientName   Trio_calib_002_run2 
Date and time
StudyDate 20050905
StudyTime 100821.656000 
SeriesTime104226.748000 
AcqTime   104209.522496 
Acquisition parameters
PulseSeq  ep_b0#0 
Protocol  DIFFUSION_HighRes 
PhEncDir  COL
EchoNo0
FlipAngle 90
EchoTime  100
InversionTime -1
RepetitionTime10100
PhEncFOV  256
ReadoutFOV256
Image information
RunNo 10
SeriesNo  11
ImageNo   1
NImageRows1024
NImageCols1024
NFrames   70
SliceArraylSize   60
IsMosaic  1
ImgPos1048.1801 1002.6923 -265.4914 
VolRes  2.   2.   2. 
VolDim128  128   60 
Vc -0.9997   0.0244   0.0005 
Vr -0.0238  -0.9764   0.2147 
Vs  0.0057   0.2147   0.9767 
VolCenter   0.   0.   0. 
TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128  60), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Numaris Version: syngo MR 2004A 4VA25A  Maj = 4, Min=2, MinMin = 5 
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix - 
 0.99970   0.02376  -0.00570  -0.49480;
-0.02443   0.97638  -0.21466  -40.55519;
 0.00047   0.21474   0.97667   12.50291;
 0.0   0.0   0.0   1.0;

FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 

Re: [Freesurfer] recon-all fatal error

[Dicamillo, Robert]

Hello Daniel,

The docker container may not be properly supporting symbolic links, i.e., 
apparently you can write files inside the container, but in your log that error 
 is the first instance of the ln command.

Could you try running it w/o using a container and see if it gets past the ln 
command?   If so, then I would ask someone at your facility to look at the 
docker configuration.  The fix for that error message in some docker postings 
is to upgrade to a newer version of docker.

- rob

On Jul 11, 2018, at 11:06 AM, Daniel Kimmel 
mailto:danielkim...@gmail.com>> wrote:


External Email - Use Caution

Hello,

I'm attempting to run basic preprocessing with reconstruction using 
fmriprep-docker.py and freesurfer. The fmriprep process completes when 
excluding freesurfer, but encounters a fatal error when including freesurfer. 
There error is:

recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018

For more details, see the log file 
/out/freesurfer/sub-18042401/scripts/recon-all-rh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:
ln: failed to create symbolic link 'rh.white.H': Operation not supported
Return code: 1

180711-01:39:51,447 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:51,452 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:54,738 cli WARNING:
Errors occurred while generating reports for participants: 18042401 (2).

The call to freesurfer is made by fmriprep, which is doing so within a docker 
container, so unfortunately I don't know the exact version of freesurfer. I'm 
using fmriprep version 1.0.13. I make the call to fmriprep from a CentOS Linux 
box:
uname -a:  Linux xxx.xxx.xxx.columbia.edu 
3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 
x86_64 GNU/Linux

I've attached:
1) the complete terminal output from fmriprep (which is reporting the output of 
freesurfer)
2) recon-all-status-rh.log
3) recon-all.log

Thanks very much for your help!
Best,
Daniel




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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] recon-all fatal error

[Dicamillo, Robert]

Hello Daniel,

The docker container may not be properly supporting symbolic links, i.e., 
apparently you can write files inside the container, but in your log that error 
 is the first instance of the ln command.

Could you try running it w/o using a container and see if it gets past the ln 
command?   If so, then I would ask someone at your facility to look at the 
docker configuration.  The fix for that error message in some docker postings 
is to upgrade to a newer version of docker.

- rob

On Jul 11, 2018, at 11:06 AM, Daniel Kimmel 
mailto:danielkim...@gmail.com>> wrote:


External Email - Use Caution

Hello,

I'm attempting to run basic preprocessing with reconstruction using 
fmriprep-docker.py and freesurfer. The fmriprep process completes when 
excluding freesurfer, but encounters a fatal error when including freesurfer. 
There error is:

recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018

For more details, see the log file 
/out/freesurfer/sub-18042401/scripts/recon-all-rh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:
ln: failed to create symbolic link 'rh.white.H': Operation not supported
Return code: 1

180711-01:39:51,447 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:51,452 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:54,738 cli WARNING:
Errors occurred while generating reports for participants: 18042401 (2).

The call to freesurfer is made by fmriprep, which is doing so within a docker 
container, so unfortunately I don't know the exact version of freesurfer. I'm 
using fmriprep version 1.0.13. I make the call to fmriprep from a CentOS Linux 
box:
uname -a:  Linux xxx.xxx.xxx.columbia.edu 
3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 
x86_64 GNU/Linux

I've attached:
1) the complete terminal output from fmriprep (which is reporting the output of 
freesurfer)
2) recon-all-status-rh.log
3) recon-all.log

Thanks very much for your help!
Best,
Daniel




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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Correct for sulcuses & ventricles size

[Bruce Fischl]

Hi John

why do you want to correct for them? They likely represent a pathological 
process, so correcting for them may remove whatever effects you are looking 
for, no? The space between the sulci and the ventricle volume won't 
directly affect surface-based analysis, but of course the sulcal widening 
likely reflects cortical atrophy that will be



cheers
Bruce


On Wed, 11 Jul 2018, John Anderson 
wrote:




External Email - Use Caution

Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have 
different degrees of
atrophy. Looking into the individual scans, the subjects are largely different 
in the space between
the sulcuses and the size of ventricles. My questions are:
1. Is there any way to correct for these differences in the surface based 
analysis?
2. Including eTIV covariate does it help in this case?
3. Does the resampling to "fsaverage" overcome the challenge of these 
differences between the
subjects? 

I appreciate any advice,
John

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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Correct for sulcuses & ventricles size

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have 
different degrees of atrophy. Looking into the individual scans, the subjects 
are largely different in the space between the sulcuses and the size of 
ventricles. My questions are:
1. Is there any way to correct for these differences in the surface based 
analysis?
2. Including eTIV covariate does it help in this case?
3. Does the resampling to "fsaverage" overcome the challenge of these 
differences between the subjects?

I appreciate any advice,
John___
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

[Jasmin Alves]

External Email - Use Caution

Hello FreeSurfer Developers,

I am trying to analyze the subfields of the hippocampus using FreeSurfer
6.0 based on the tutorial, "Segmentation of hippocampal subfields".
However, several errors come up when I run:

recon-all -s 102 -hippocampal-subfields-T1

#@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT
2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18
PDT 2018
dirname: Command not found.
pwd: Command not found.
pwd: Command not found.
/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

I have searched through the list to see if anyone else has had this issue
but to no avail.

Version:

freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

OS: X V 10.9.5

Thanks!
Jasmin


-- 
Jasmin Alves
Doctoral Candidate
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] [TRACULA] eddy_correct /affine registration matrices / motion/ eddy currents

[Daumail, Loic Jean]

Dear FreeSurfer experts,

I would like to understand better the principle of eddy_correct:

-in which way the eddy currents caused by motion are set apart from the eddy 
currents caused by fast switching diffusion-encoding gradients?

-and then, how are the affine registration matrices reflecting motion computed  
by eddy_correct considering the previous issues?

-does eddy_correct even computes these affine registration 
matrices(dwi.ecclog)? or is it another tool of dmri_motion?


Thanks,

Loïc Daumail
Graduate intern at Athinoula A. Martinos Center for Biomedical Imaging MGH/HST
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] non-stationarity in CTh maps

[Antonin Skoch]

External Email - Use Caution


Dear experts,


following on this old thread, do you have any new knowledge on the possible 
severity of non-stationarity in cortical-thickness maps and its effect on 
permutation-based cluster-extent inference? Given current status of 
development, is here a possibility to estimate it/correct for it?


Regards,


Antonin Skoch



Hi Hugo, they are assumed to be stationary. I've never tried to figure out how 
much of a problem this is.doug

On 7/25/12 6:03 PM, Hugo Baggio wrote:
Dear all,I have been performing cortical thickness analyses and as far as I 
understand the thickness maps are non-stationary (please correct me if I'm 
wrong). I have two questions: 1. How susceptible is Monte Carlo clusterwise 
correction to this(should I expect clusters at smoother areas to be bigger?)? 
2. Does FS perform some sort of correction to this non-stationarity or are 
images assumed to be stationary at statistical analyses?Thanks a lot for your 
help!

Hugo___
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Re: [Freesurfer] Errors preprocess

[Boyd, Emma]

Hi Seonjoo,


What directory are you in when you run preproc-sess? You should run this 
command from the data/ dir.


Emma



-

Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lee, Seonjoo 

Sent: Wednesday, July 11, 2018 8:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors preprocess


External Email - Use Caution

Dear Freesurfer experts,

I tried to run preproc-sess but did not have much luck to make it work.



I converted resting fmri file into .nii, and I created the following directory 
structure and it’s stored under /data/sub1/rest/001/fMRI.nii:





/data

/data/sub1

/data/sub1/rest

/data/sub1/rest/001/

/data/sub1/rest/001/fMRI.nii





Then I ran



preproc-sess -s sub1 -fsd rest -surface $FSAVERAGE_DIR/fsaverage lhrh -mni305 
-fwhm 5 -per-run



And I kept getting the following error message:



ERROR: cound not find session sub1



To run freesurfer I specified SUBEJCTS_DIR as /data (I don’t think it matters, 
though…)





export FREESURFER_HOME=/Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh

SUBJECTS_DIR=/data



Any suggestion to make it work?

Thanks.

-Seonjoo












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[Freesurfer] Errors preprocess

[Lee, Seonjoo]

External Email - Use Caution

Dear Freesurfer experts,
I tried to run preproc-sess but did not have much luck to make it work.

I converted resting fmri file into .nii, and I created the following directory 
structure and it’s stored under /data/sub1/rest/001/fMRI.nii:


/data
/data/sub1
/data/sub1/rest
/data/sub1/rest/001/
/data/sub1/rest/001/fMRI.nii


Then I ran


preproc-sess -s sub1 -fsd rest -surface $FSAVERAGE_DIR/fsaverage lhrh -mni305 
-fwhm 5 -per-run



And I kept getting the following error message:



ERROR: cound not find session sub1



To run freesurfer I specified SUBEJCTS_DIR as /data (I don’t think it matters, 
though…)




export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
SUBJECTS_DIR=/data


Any suggestion to make it work?

Thanks.

-Seonjoo








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[Freesurfer] Petsurfer: Longitudinal GTM stats?

[Elijah Mak]

External Email - Use Caution

Hi Freesurfer Team and Doug,

Is there any way to derive the gtmstats from Petsurfer within a longitudinal 
design? 

Could I get your take on the steps below?

1. Extract GTM stats from each PET time-point (registered to the closest 
structural MRI in time).
2. Manually compute the percent change per region across time-points.

Alternatively, would it be more ideal to resample the PET data to the surfaces 
at each time point before extracting the MGX-based ROI PET data with 
mri_segstats? With this approach, it would be possible to use the longitudinal 
commands, right?

Thanks!
Elijah

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