Re: [Freesurfer] Building from source #3 -- dynamic binding

[Dicamillo, Robert]

Hello Yaroslav,

I believe there is already an option that can be set at configure time to build 
dynamical;ly, though
I have not tried it. e.g., maybe it causes the libraries that
Freesurfer builds internally to be built as shared instead of static.

However, at least in out nightly builds, the freesurfer binaries link
dynamically with the linux system libs.  It looks like there are about 130
linux system libraries referenced by all the ELF files in a built freesurfer 
tree.

By comparison I think there may be no more then 15 static libs built and linked
against inside the freesurfer tree.  While these could be built shared, I’m
not sure there is an expectation that end users should be able to replace/update
these libs within a release of Freesiurfer.

- rob


> On Mar 29, 2018, at 4:36 PM, Yaroslav Halchenko 
>  wrote:
> 
> Dear FreeSurfer developers,
> 
> I would like to pick up on this elderly theme by wondering:
> 
> Would you be philosophically opposed against patches/pull requests
> which introduce dynamic linking for freesurfer build?  
> 
> Would anyone from the FreeSurfer team be interested to pursue such
> an effort?
> 
> The idea is to try to reincarnate the effort of pulling
> functionality/binary-code which is now spread/duplicated across many
> distributed statically linked binaries, into a set of (internal)
> libraries.  Benefits IMHO are numerous, starting from
> 
> - smaller binary distribution
> 
> - consistency (replacing one patched binary copy but leaving the
>  other copies which linked statically unpatched)
> 
> - ...
> 
> 
> Cheers,
> 
> On Sun, 21 Feb 2016, Yaroslav Halchenko wrote:
>> On Sun, 21 Feb 2016, zkauf...@nmr.mgh.harvard.edu wrote:
> 
>>> This topic gets brought up occasionally and their are valid arguments
>>> to both sides. One reason we have hesitated to use dynamic libs is the
>>> partly due to freesurfers long release cycle (all subjects that are
>>> part of a study need to be performed all on the same version). This
>>> long release cycle sometimes necessitates fixes to a particular binary
>>> in the stream, which users are then free to use. Although this is a
>>> less than ideal release strategy, it is the reality of the situation.
>>> And if we linked against dynamic libs than any time a binary was
>>> updated, ALL those libs, would need to be updated,
>>> which in turn would affect all binaries which link against them. 
> 
>> AFAIK it is exactly the other way around ;) Please correct me if I
>> am wrong.
> 
>> With static inclusion of code, if the fix is in the code which is shared
>> among binaries, you will need  to provide new copies for all those
>> effected binaries so they come with new copies of that code.   Only if
>> the fix is within code specific to the binary -- only that binary
>> indeed.
> 
>> In case if that 'fixed' code being a part of an internal dynamic library
>> [*], you would need to provide only a copy of that library, and binaries
>> linked against it can stay original since they just dynamically load
>> that code from the library and do not carry broken code.   If it
>> is a fix to the code specific to the binary -- situation is just the
>> same as with static linking.
> 
>> [*] under assumption that the fix doesn't entail changing  API/ABI.  In
>> case if those change -- indeed adjustment/rebuild of dependent binaries
>> would be necessary.  BUT such situations come much less often than just
>> fixes of the code without changing data structures and function
>> interfaces. And in your case, even if that happens, it is just a matter
>> again of uploading all those affected binaries (as you would do with
>> static linking) + the dynamic library.  And again, I think, even if a
>> binary uses some functionality of the library, but not a 'fixed'
>> function, it could as well stay without 'update' while linking to
>> the new dyn library.
> 
>> That is the primary reason why Linux distributions rely on dynamic
>> libraries and reusing system-wide installed artifacts (e.g. java script
>> "libraries", Python modules, etc) as often as possible -- to fix a
>> vulnerability in the code of a core library/artifact requires just
>> upload of the fixed library/artifact without rebuilding all binaries (or
>> replacing all copies of artifacts) which could have potentially absorbed
>> that code via static "linking".  Could you imagine the chaos if
>> libc was statically included in every binary and then security fix
>> was needed to propagate to all 30,000 packages? ;)
> 
> 
>>> I suppose only newly released binaries could be static,
>>> but their may be unintended consequences that Im not thinking of at the
>>> moment.
> 
>>> Im open to conversing about this, and appreciate any constructive feedback
>>> on improving our release model. 
> 
>> Well -- I can't recommend anything new really, and just repeat my
>> whining: modularize just a bit (e.g. separate package for heavy data
>> pieces which rarely change + dynamic 

[Freesurfer] Freesurfer and crypt

[Bennet Fauber]

I have a couple of users here who are reporting that on machines with
FIPS enabled, which in turn disables certain cryptographic functions,
FreeSurfer core dumps with a call to the crypt() function, which FIPS
disables.

Someone speculated based on output from strace that this is FreeSurfer
possibly attempting to validate its license.

Is this a known problem?  Is there a solution?

We have a university compliance office and possibly similar people
from our local VA who are insisting that FIPS be enabled.

If you need more information, please let me know and I will try to
obtain it for you.

Thanks,-- bennet
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[Freesurfer] Building from source #3 -- dynamic binding

[Yaroslav Halchenko]

Dear FreeSurfer developers,

I would like to pick up on this elderly theme by wondering:

Would you be philosophically opposed against patches/pull requests
which introduce dynamic linking for freesurfer build?  

Would anyone from the FreeSurfer team be interested to pursue such
an effort?

The idea is to try to reincarnate the effort of pulling
functionality/binary-code which is now spread/duplicated across many
distributed statically linked binaries, into a set of (internal)
libraries.  Benefits IMHO are numerous, starting from

- smaller binary distribution

- consistency (replacing one patched binary copy but leaving the
  other copies which linked statically unpatched)

- ...


Cheers,

On Sun, 21 Feb 2016, Yaroslav Halchenko wrote:
> On Sun, 21 Feb 2016, zkauf...@nmr.mgh.harvard.edu wrote:

> > This topic gets brought up occasionally and their are valid arguments
> > to both sides. One reason we have hesitated to use dynamic libs is the
> > partly due to freesurfers long release cycle (all subjects that are
> > part of a study need to be performed all on the same version). This
> > long release cycle sometimes necessitates fixes to a particular binary
> > in the stream, which users are then free to use. Although this is a
> > less than ideal release strategy, it is the reality of the situation.
> > And if we linked against dynamic libs than any time a binary was
> > updated, ALL those libs, would need to be updated,
> > which in turn would affect all binaries which link against them. 

> AFAIK it is exactly the other way around ;) Please correct me if I
> am wrong.

> With static inclusion of code, if the fix is in the code which is shared
> among binaries, you will need  to provide new copies for all those
> effected binaries so they come with new copies of that code.   Only if
> the fix is within code specific to the binary -- only that binary
> indeed.

> In case if that 'fixed' code being a part of an internal dynamic library
> [*], you would need to provide only a copy of that library, and binaries
> linked against it can stay original since they just dynamically load
> that code from the library and do not carry broken code.   If it
> is a fix to the code specific to the binary -- situation is just the
> same as with static linking.

> [*] under assumption that the fix doesn't entail changing  API/ABI.  In
> case if those change -- indeed adjustment/rebuild of dependent binaries
> would be necessary.  BUT such situations come much less often than just
> fixes of the code without changing data structures and function
> interfaces. And in your case, even if that happens, it is just a matter
> again of uploading all those affected binaries (as you would do with
> static linking) + the dynamic library.  And again, I think, even if a
> binary uses some functionality of the library, but not a 'fixed'
> function, it could as well stay without 'update' while linking to
> the new dyn library.

> That is the primary reason why Linux distributions rely on dynamic
> libraries and reusing system-wide installed artifacts (e.g. java script
> "libraries", Python modules, etc) as often as possible -- to fix a
> vulnerability in the code of a core library/artifact requires just
> upload of the fixed library/artifact without rebuilding all binaries (or
> replacing all copies of artifacts) which could have potentially absorbed
> that code via static "linking".  Could you imagine the chaos if
> libc was statically included in every binary and then security fix
> was needed to propagate to all 30,000 packages? ;)


> > I suppose only newly released binaries could be static,
> > but their may be unintended consequences that Im not thinking of at the
> > moment.

> > Im open to conversing about this, and appreciate any constructive feedback
> > on improving our release model. 

> Well -- I can't recommend anything new really, and just repeat my
> whining: modularize just a bit (e.g. separate package for heavy data
> pieces which rarely change + dynamic libraries, you already have that
> bundle of externals you could deploy and reuse), and then you can
> easily release not just "binary patches" but entire bugfix releases of
> the codebase since they will probably be a fraction of the current size.
> That is AFAIK how anything is released these days really ;)

> NB. somewhat crazier scheme could be -- release binaries via git-annex,
> with upgrades constituting "git pull; git annex get . " ;) It
> would become especially efficient in case of dynamic internal
> libraries, since fetching a bugfix release would be to fetch only
> affected dynamic libraries and not all affected binaries linking against
> them.

> > But I would prefer to take the
> > conversation offline as it gets overly technical rather quick.

> ah (I was replying inline without reading all the way till the
> end, sorry ;)), then this will be the last one then on this mailing list
> in this series.  Could there may be a freesurfer-devel mailing list to

[Freesurfer] which dev version for amygdala segmentation

[Anik Dar]

Hi All,

How do I download reqd. files / FS developmental version to run
hippocampal/amygdala pipeline as described in the wiki

https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

I tried downloading the el capitan version of the development version of
freesurfer from the

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

and I cant find any code segmentHA_T1.sh

Can anyone help,

Thanks

Ani
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Re: [Freesurfer] Hemodynamic Lag Shift

[Sarah Cole]

Thanks, Doug.

I added (-4s) delay and plotted the data but I got the same delay as no
shift. Also I did (+4) delay and lost most of the activation.

Do you have any recommendations?

Thanks,
Sarah

On Wed, Mar 28, 2018 at 4:39 PM, Douglas N. Greve 
wrote:

> You can use the -delay flag in mkanalysis-sess
>
> doug
>
>
> On 03/28/2018 05:35 PM, Sarah Cole wrote:
> > Hi Doug,
> >
> > I have a block design experiment. After analyzing the data and
> > plotting the response magnitude across the TRs, we see that there is a
> > systematic lag in the response. For example, in a 16s block (TR=2s),
> > at TR-1 and TR-2 the response goes down and then starts rising from
> > TR-3. This is consistent across the subjects and blocks.
> >
> > We used to shift our raw data by 2 TRs when we were using SPM.
> >
> > How can we do this in FreeSurfer?
> >
> > Thank you,
> >
> > Sarah
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
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[Freesurfer] Longitudinal data from different sequences and scanners

[James Gullickson]

 All,

Our lab is working with longitudinal (two time points) data from a cohort
of around 130 individuals. We are attempting to make comparisons between
time points 1 and 2 on measures like total brain volume, ventricular
volume, ventricle-brain-ratio, and cortical thickness. However, we have run
into an issue--we are seeing net increases in cortical thickness and total
brain volume over time (which seems biologically implausible, given our age
range of ~30-60 yrs old). We think it may have something to do with the
fact that the T1w data from each time point was acquired with slightly
different parameters and on different scanners, possibly leading to a
rounding error in quantification of volumes/thickness. Timepoint 1 data are
1.0mm isotropic and were acquired on a 3T Siemens Tim Trio with 12ch
headcoil. Timepoint 2 data are 0.8mm isotropic and were acquired on the
same scanner, but which went through an upgrade to a Prisma Fit between
timepoints, using a 32ch coil.

Currently we have been comparing data from the cross sectional stream. We
would like to use the longitudinal stream if that would improve results,
but we saw this post that cautioned against it: https://www.mail-archive.c
om/freesurfer@nmr.mgh.harvard.edu/msg52992.html

What would be your recommendation for comparing this data longitudinally?
Any thoughts on why we are seeing net increases in volume/thickness, and
how to avoid that? One idea we had was perhaps degrading each image by
rigid co-registration and then bringing each image into the halfway space
between the two (as FSL's SIENA does).

Thanks,

James
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[Freesurfer] mirroring fsaverage labels between hemispheres

[Abigail Noyce]

Hi, I have pored over (I think) all of the mailing list postings about
cross-hemisphere mapping and I can't quite figure out how to do this.

I have a bunch of labels on fsaverage, and I want to be able to
check/visualize the relationship between lh and rh versions of the labels.

I can do mri_label2label to map from fsaverage to fsaverage_sym, but that
doesn't do the right thing, and fsaverage doesn't have the same kind of
xhemi registration structure that "normal" subjects get with surfreg
--xhemi. I guess I could back-project onto a normal subject and then
project to fsaverage_sym, but that seems like an unnecessary step.

How can I get mirror-projected labels from fsaverage on fsaverage_sym?

Thanks!
Abby
-- 
Abigail L. Noyce, Ph.D.
Psychological & Brain Sciences
Boston University

ano...@bu.edu
617-440-3640
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Re: [Freesurfer] defining input images in a for-loop in recon-all

[Bruce Fischl]

yes, that would work
cheers
Bruce

On Thu, 29 Mar 2018, Darko Komnenić wrote:


Hi Bruce,
thanks for the reply. I only have one acquisition per subject. I guess
I can make a separate text file with a list of paths to dicoms and
then somehow try to pair the path and the subject name in the
recon-all command.



From: Bruce Fischl 
Subject: Re: [Freesurfer] defining input images in a for-loop in
recon-all
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi Darko

sorry, you need to sort this out yourself as there is no way for us to
know where the dicoms are. An alternative is to create each subject dir,
create the 00?.mgz files (if you have more than one acquistion) in the
/mri/orig dir, then run recon-all without the -i flag. If you use
-i you need to figure out a way to find one slice in the correct dicom
series for each subject.

cheers
Bruce


On
Thu, 29 Mar 2018, Darko Komneni? wrote:


Dear experts,
I would like to run a for-loop in FreeSurfer 5.1. so that I can have
multiple subjects analyzed over
the holiday, without having to come to the lab and start each of them
myself. I searched the
previous emails in this list and know that I can make a file with a
subject list, and then have the
loop go through that file.
I was wondering, however, how to handle the -i part of recon-all command?
Each subject in a loop
needs to have one brain image assigned - I don't think FreeSurfer will
know where to look for images
just by telling it what the subject name is.
Thanks in advance for any help!

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Re: [Freesurfer] defining input images in a for-loop in recon-all

[Darko Komnenić]

Hi Bruce,
thanks for the reply. I only have one acquisition per subject. I guess
I can make a separate text file with a list of paths to dicoms and
then somehow try to pair the path and the subject name in the
recon-all command.


> From: Bruce Fischl 
> Subject: Re: [Freesurfer] defining input images in a for-loop in
>   recon-all
> To: Freesurfer support list 
> Message-ID:
>   
> Content-Type: text/plain; charset="utf-8"
>
> Hi Darko
>
> sorry, you need to sort this out yourself as there is no way for us to
> know where the dicoms are. An alternative is to create each subject dir,
> create the 00?.mgz files (if you have more than one acquistion) in the
> /mri/orig dir, then run recon-all without the -i flag. If you use
> -i you need to figure out a way to find one slice in the correct dicom
> series for each subject.
>
> cheers
> Bruce
>
>
> On
> Thu, 29 Mar 2018, Darko Komneni? wrote:
>
>> Dear experts,
>> I would like to run a for-loop in FreeSurfer 5.1. so that I can have
>> multiple subjects analyzed over
>> the holiday, without having to come to the lab and start each of them
>> myself. I searched the
>> previous emails in this list and know that I can make a file with a
>> subject list, and then have the
>> loop go through that file.
>> I was wondering, however, how to handle the -i part of recon-all command?
>> Each subject in a loop
>> needs to have one brain image assigned - I don't think FreeSurfer will
>> know where to look for images
>> just by telling it what the subject name is.
>> Thanks in advance for any help!
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Re: [Freesurfer] Information on FS-FAST

[Douglas N. Greve]

yes, you have to create a segmentation in $SUBJECTS_DIR/$subject/mri in 
the same format as aseg.mgz, then when you run fcseed-config, specify 
-seg yourseg.mgz -segid yoursegid



On 03/29/2018 05:36 AM, Piero Chiacchiaretta wrote:
>
> Thanks Doug.
>
> My goaI is to perform a FC analysis of cerebellum subregions using 
> FS-FAST. I understand that FS do not permit the segmentazion for 
> 601-602. Anyway, do you think that I can use as seed the cerebellar 
> regions defined by Buckner et 
> al.(http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011)? 
> Have you alternative way or any suggestion?
>
> Best regards
>
> Piero
>
>
> Piero Chiacchiaretta, PhD
> Institute for Advanced Biomedical Technologies - ITAB -
> University “G. d’Annunzio” of Chieti - Pescara
> Department of Neuroscience, Imaging and Clinical Sciences
> Via dei Vestini, 31
> 66013 Chieti, Italy
>
> tel: 39-0871-3556919 
> fax: 39-0871-3556930 
> e-mail: p.chiacchiare...@unich.it 
>
>
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Re: [Freesurfer] convert labels to volume in MNI?

[Douglas N. Greve]

By using -reg $FREESURFER_HOME/average/mni152.register.dat you are 
indicating that the input label is in fsaverage space. You need to have 
a registration from your source space (VPNL) to the MNI152. If you have 
a whole brain in VPNL, then you can run recon-all on it to generate 
surfaces. Do the same thing with the MNI152, then use mri_label2label 
with surface registration to map between the two.

On 03/29/2018 07:08 AM, gj wrote:
> The labels are from Stanford VPNL's vcAtlas (cytorchitectonic atlas of
> the human ventral visual system).
>
> Does this mean that my mri_label2vol command which I posted earlier
> looks okay?
>
> To doublecheck my files in freeview, I did a simple
>
> freeview -v $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
> $wd/MPM_rh.FG2.label.nii \
>   -l $VC/MPM_rh.FG2.label &
>
> where *.label.nii is the output from the mri_label2vol command I ran.
> I couldn't figure out how you load the ROI NIFTI mask as an ROI so that
> you can see it on top of the structural template -- the -l switch seems
> to only take label formats?
>
> In the attached screenshot freesurfer_prob_1.png, you see the yellow ROI
> corresponding to one label (fusiform gyrus) from the vcAtlas, which
> appears to be incorrectly rotated by 90deg.
>
> The second attached screenshot freesurfer_prob_1.png shows the output
> from mri_label2vol as a white cluster, which if all were right, I would
> assume would overlap with the yellow cluster corresponding to the
> original atlas label...but I guess the volumetric ROI looks roughly in
> the right place, but still not quite right? Why does it look so
> different in mricron?
>
> Sorry for flood of newbie Qs
> Thank you!
> Gina
>
>
>
> -- FWD'd msg --
> Douglas N. Greve Wed, 28 Mar 2018 10:18:40 -0700
>
> what is your freeview command line? In the mri_label2vol command below,
> where does the label come from?
>
>
>
> On 2018-03-28 19:11, gj wrote:
>> Hi,
>>
>> I loaded the 2mm MNI152 template and the mri_label2vol outputs in
>> mricron, and I saw that the labels are completely outside the template.
>> So, I know now to use freeview rather than the deprecated tkmedit so I
>> can also load the original atlas labels to check against (using the 2mm
>> MNI152 template as background) -- in any case, I don't even see the
>> labels, I guess because the ROIs/masks lie outside the display. I'm also
>> not sure what the equivalent of tkmedit's overlay-reg is for freeview? I
>> assume my not loading one is why I get the error, "Label coordinate out
>> of bound" when I try and load the original atlas labels (in fsaverage
>> space) on the MNI152 template?
>>
>> Thank you!
>> Gina
>>
>> P.S. Can't find a straightforward way to reply with the entire thread
>> when receiving only a digest from the listserv -- reply to the digest
>> takes the freesurfer-request address rather than the list address and
>> the button on the website for archives only gives the option of replying
>> directly to the person who posted)...what am I missing?
>>
>>
>> --
>>
>> Douglas Greve dgreve at mgh.harvard.edu
>> Tue Mar 27 14:01:16 EDT 2018
>>
>> how are you verifying that it is not in the right place? You should view
>> it on the 2mm MNI152 using freeview. Also, your label should be a label
>> in fsaverage space.
>>
>>
>> On 3/27/18 9:52 AM, gj wrote:
>>> Hi,
>>>
>>> Newbie questionI want to take FreeSurfer labels (from an atlas in
>>> fsaverage space) and convert it into a volumetric NIFTI mask. I ran the
>>> following command, but I must be missing something because the output is
>>>not in the right space (far too posterior):
>>>
>>>  $FREESURFER_HOME/bin/mri_label2vol \
>>> --label $ll \
>>> --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
>>> --reg $FREESURFER_HOME/average/mni152.register.dat \
>>> --fillthresh .5 \
>>> --o $wd/${ll}.nii
>>>
>>> Am I perhaps supposed to first create the volumetric file without
>>> mapping into MNI space and then use tkregister2?
>>>
>>> Thanks in advance for any help or advice!
>>> Gina
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] defining input images in a for-loop in recon-all

[Bruce Fischl]

Hi Darko

sorry, you need to sort this out yourself as there is no way for us to 
know where the dicoms are. An alternative is to create each subject dir, 
create the 00?.mgz files (if you have more than one acquistion) in the 
/mri/orig dir, then run recon-all without the -i flag. If you use 
-i you need to figure out a way to find one slice in the correct dicom 
series for each subject.


cheers
Bruce


On 
Thu, 29 Mar 2018, Darko Komnenić wrote:



Dear experts,
I would like to run a for-loop in FreeSurfer 5.1. so that I can have multiple 
subjects analyzed over
the holiday, without having to come to the lab and start each of them myself. I 
searched the
previous emails in this list and know that I can make a file with a subject 
list, and then have the
loop go through that file.
I was wondering, however, how to handle the -i part of recon-all command? Each 
subject in a loop
needs to have one brain image assigned - I don't think FreeSurfer will know 
where to look for images
just by telling it what the subject name is.
Thanks in advance for any help!

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Re: [Freesurfer] Information on FS-FAST

[Piero Chiacchiaretta]

Thanks Doug.
My goaI is to perform a FC analysis of cerebellum subregions using FS-FAST. I 
understand that FS do not permit the segmentazion for 601-602. Anyway, do you 
think that I can use as seed the cerebellar regions defined by Buckner et 
al.(http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011)? Have 
you alternative way or any suggestion?
Best regards
Piero

Piero Chiacchiaretta, PhD
Institute for Advanced Biomedical Technologies - ITAB -
University “G. d’Annunzio” of Chieti - Pescara
Department of Neuroscience, Imaging and Clinical Sciences
Via dei Vestini, 31
66013 Chieti, Italy

tel: 39-0871-3556919
fax: 39-0871-3556930
e-mail: p.chiacchiare...@unich.it
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[Freesurfer] "preproc-sess" with intermediate volume

[David Sánchez Bestué]

Dear all,

I have a problem with the command:
"preproc-sess"

I wanted to use the Registration option to add an intermediate volume. The only 
documentation I could find about it was the one that appears with the command: 
"preproc-sess --help"

Registration options
  -init-fsl : use fsl to initialize bbr registration
  -init-spm : use spm to initialize bbr registration (needs matlab)
  -init-header : use geometry to initialize bbr registration
  -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem


I used the last flag in my line as follows:

preproc-sess -s session_1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run 
-bbr-int ifsd istem

I got this error:

ERROR: could not determine file for ifsd/001/istem


It seems that the path is not working but I do not why. The relevant paths are 
this:

session_1/bold/001/f.nii
session_1/ifsd/001/istem/orig.mgz

Any help would be really appreciated!

Thank you all

Bests,

David




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[Freesurfer] defining input images in a for-loop in recon-all

[Darko Komnenić]

Dear experts,
I would like to run a for-loop in FreeSurfer 5.1. so that I can have
multiple subjects analyzed over the holiday, without having to come to the
lab and start each of them myself. I searched the previous emails in this
list and know that I can make a file with a subject list, and then have the
loop go through that file.
I was wondering, however, how to handle the -i part of recon-all command?
Each subject in a loop needs to have one brain image assigned - I don't
think FreeSurfer will know where to look for images just by telling it what
the subject name is.
Thanks in advance for any help!
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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
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
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