Re: [Freesurfer] brain mask without CSF ...

[Franklin, Crystal G]

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3


 Original message 
From: "Greve, Douglas N.,Ph.D." 
Date: 10/10/19 5:56 PM (GMT-06:00)
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] brain mask without CSF ...

You will have to do it manually. You can create a binary CSF mask from the 
aseg.mgz using mri_binarize. Don't use 702 and 703 -- those refer to "FSL-FAST" 
not "FS-FAST". Try using the --vcsf flag to mri_binarize (ventricular csf). 
Then use mri_label2vol to map it into the functional space. Once there,  mask 
the brain.nii.gz files (found in fsd/masks and fsd/RRR/masks where RRR is each 
run) using
cp brain.nii.gz brain.orig.nii.gz
fscalc yourmask.nii.gz not and brain.orig.nii.gz -o brain.nii.gz
The rerun selxavg3-sess. It should automatically update from the brain mask 
point in the pipeline

On 10/8/2019 12:56 PM, 
stefano.silv...@libero.it wrote:

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Dear FreeSurfer Experts,

I am running a functional analysis of subcortical structures using FS-FAST 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a 
brain mask excluding CSF; would it be possible using some option/flag in 
'preproc-sess'?

or should I do it manually? maybe using a command like that?


mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o 
$sbjdir/mri/GM-WM_mask.mgz


because I saw in FreeSurferColorLUT.txt the following definitions:

702 GrayMatter-FSL-FAST 205 62 78 0
703 WhiteMatter-FSL-FAST 0 225 0 0

or is there another strategy?

thanks in advance
best
stefano silvoni



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Re: [Freesurfer] brain mask without CSF ...

[Greve, Douglas N.,Ph.D.]

You will have to do it manually. You can create a binary CSF mask from the 
aseg.mgz using mri_binarize. Don't use 702 and 703 -- those refer to "FSL-FAST" 
not "FS-FAST". Try using the --vcsf flag to mri_binarize (ventricular csf). 
Then use mri_label2vol to map it into the functional space. Once there,  mask 
the brain.nii.gz files (found in fsd/masks and fsd/RRR/masks where RRR is each 
run) using
cp brain.nii.gz brain.orig.nii.gz
fscalc yourmask.nii.gz not and brain.orig.nii.gz -o brain.nii.gz
The rerun selxavg3-sess. It should automatically update from the brain mask 
point in the pipeline

On 10/8/2019 12:56 PM, 
stefano.silv...@libero.it wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am running a functional analysis of subcortical structures using FS-FAST 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a 
brain mask excluding CSF; would it be possible using some option/flag in 
'preproc-sess'?

or should I do it manually? maybe using a command like that?


mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o 
$sbjdir/mri/GM-WM_mask.mgz


because I saw in FreeSurferColorLUT.txt the following definitions:

702 GrayMatter-FSL-FAST 205 62 78 0
703 WhiteMatter-FSL-FAST 0 225 0 0

or is there another strategy?

thanks in advance
best
stefano silvoni



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Re: [Freesurfer] fsaverage label into functional space

[Adam Martersteck]

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To confirm, your label is starting on the fsaverage surface. You can open
tksurfer fsaverage ?h pial and open the label and it shows up?

From my experience using fcseed-sess & fcseed-config using FS v6.0.0 what
you want to do is move the label from fsaverage -> subject native surface
-> subject native T1 volume and it will take care of the rest

So you would run:
label=your_label (without the .label at the end)
subject=your_new_subject
hemi=lh (or rh)

mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/$label.label
--trglabel $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
--srcsubject fsaverage --hemi $hemi --srchemi $hemi --trghemi $hemi
--regmethod surface
mri_label2vol --label $SUBJECTS_DIR/$subject/label/$label.label --temp
$SUBEJCTS_DIR/$subject/mri/brainmask.mgz --fill-ribbon --subject $subject
--hemi $hemi --regheader $SUBJECTS_DIR/$subject/mri/brainmask.mgz --o
$SUBJECTS_DIR/$subject/mri/$label.mgz

The new file is what you would input as the "-seg $label.mgz" in the
fcseed-config command

On a related note -- in my tests of -proj-frac vs. -fill-ribbon == if you
want the full ROI from edge of the white surface to the pial surface you
should use -fill-ribbon -- see attached screenshot

[image: projfrac_vs_fill-ribbon.png]

On Thu, Oct 10, 2019 at 12:03 PM Lauri Tuominen  wrote:

> External Email - Use Caution
>
> Dear FreeSurfers!
>
> I would like to confirm something before I proceed with my analyses. I
> think I am just confused again.
>
> I am doing resting state analysis using fsfast. I am trying to use a label
> defined in the fsaverage space as a seed using the fcseed-config &
> fcseed-sess commands. Now these commands say that the label should be in
> fuctional space, which I gather is the space of the f.nii.
>
> So in order to move the label into functional space I say:
>
> mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label
> --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01
> --hemi lh --temp ${projectdir}/${sessionj}/rest/001/f.nii --fill-ribbon
> --reg ${projectdir}/${session}/rest/register.dof6.lta
>
> To my surprise, the voxel size here corresponds to the anatomical
> (orig.mgz) but not the functional space (f.nii). To test this further I
> did:
>
> mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label
> --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01
> --hemi lh --temp $SUBJECTS_DIR/$/${sessionj}/mri/orig.mgz --fill-ribbon
> --reg ${projectdir}/${session}/rest/register.dof6.lta
>
> And I get exactly the same ROI in the volume.
>
> So just to confirm, is this what I want for the fcseed -commands?
>
> Thank you so much again!
>
> Lauri Tuominen
>
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Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

[Greve, Douglas N.,Ph.D.]

I think that the wm edits should have worked. Can you load the rh.orig.nofix 
and rh.orig to see if they encompass your edits? If not, then maybe your did 
not re-run it properly.

On 10/8/2019 12:22 PM, Xiaoqian Yan wrote:

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Dear Freesurfer experts,

I am trying to do the segmentation on a patient's T1 image. I did not get error 
messages running the 'recon-all' (recon-all -i T1.nii -subjid PatientName 
-all), but the segmentation over the right occipital lobe was imperfect, which 
caused failures to map the functional activations in this region onto the 
surface.

I tried to manually edit the wm.mgz several times, but the output did not 
change a lot (please see the attached image). The patient had depth EEG 
electrodes implanted in this region before, so there is a thermal lesion which 
I thought could have caused the bad segmentation.  Do you have any ideas about 
what I can do next, or it is possible for you to help me editing the data?

Thanks in advance, best wishes

Xiaoqian



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Re: [Freesurfer] fsaverage label into functional space

[Greve, Douglas N.,Ph.D.]

This appears to be a bug in mri_label2vol when you specify a surface. 
Instead, you can create a volume in the conformed space, and then use 
mri_label2vol with that volume as the --seg input. BTW, you should use 
mri_label2label to map from fsaverage into the individual subject space, 
then do the two calls to mri_label2vol.
doug

On 10/10/2019 1:02 PM, Lauri Tuominen wrote:
>  External Email - Use Caution
>
> Dear FreeSurfers!
>
> I would like to confirm something before I proceed with my analyses. I think 
> I am just confused again.
>
> I am doing resting state analysis using fsfast. I am trying to use a label 
> defined in the fsaverage space as a seed using the fcseed-config & 
> fcseed-sess commands. Now these commands say that the label should be in 
> fuctional space, which I gather is the space of the f.nii.
>
> So in order to move the label into functional space I say:
>
> mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o 
> lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01  --hemi lh 
> --temp ${projectdir}/${sessionj}/rest/001/f.nii --fill-ribbon --reg 
> ${projectdir}/${session}/rest/register.dof6.lta
>
> To my surprise, the voxel size here corresponds to the anatomical (orig.mgz) 
> but not the functional space (f.nii). To test this further I did:
>
> mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o 
> lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01  --hemi lh 
> --temp $SUBJECTS_DIR/$/${sessionj}/mri/orig.mgz --fill-ribbon --reg 
> ${projectdir}/${session}/rest/register.dof6.lta
>
> And I get exactly the same ROI in the volume--p.
>
> So just to confirm, is this what I want for the fcseed -commands?
>
> Thank you so much again!
>
> Lauri Tuominen
>
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Re: [Freesurfer] Assign different number in FreeSurferColorLUT

[Greve, Douglas N.,Ph.D.]

The easiest thing is probably to set the output value when running mri_binarize 
with the --binval option. Eg, left amygdala would be --binval 18

On 10/10/2019 6:09 PM, Gwang-Won Kim wrote:

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Hi there,

I made the 3 ROIs (Thalamus, amygdala, putamen) using "mri_binarize".
Then, I opened "FreeView" to show the 3 ROIs (3 volumes).
I want to show 3 ROIs as different colors in FreeView.
I tried to apply to FreeSurferColorLUT in FreeView but 3 volumes (3 ROIs) have 
the color of number #1 in FreeSurferColorLUT. How do I assign different number 
of FreeSurferColorLUT in 3 volumes?

Thank you,
Gwang-Won Kim



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[Freesurfer] Assign different number in FreeSurferColorLUT

[Gwang-Won Kim]

External Email - Use CautionHi there, I made the 3 ROIs (Thalamus, amygdala, putamen) using "mri_binarize".Then, I opened "FreeView" to show the 3 ROIs (3 volumes). I want to show 3 ROIs as different colors in FreeView.I tried to apply to FreeSurferColorLUT in FreeView but 3 volumes (3 ROIs) have the color of number #1 in FreeSurferColorLUT. How do I assign different number of FreeSurferColorLUT in 3 volumes? Thank you,Gwang-Won Kim













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Re: [Freesurfer] Freesurfer 6 current state of submillimeter processing

[Greve, Douglas N.,Ph.D.]

Use the patch

On 10/10/2019 11:07 AM, Daniel Westfall wrote:

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Hi Everyone,

I just wanted to double check the current state of processing T3 submillimeter 
data with Freesurfer 6. We have two studies: one with 0.9 mm isotropic and the 
other with 0.8 mm isotropic. After doing some investigating, I found that there 
is either the option to run recon-all with the -hires flag 
(https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon) or I found that 
on the release notes for Freesurfer 6 there is a patch 
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/). I 
would guess that the patch method is the most recent version that I should use?

Thank you for the assistance.

Best,
Daniel



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Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Hoopes, Andrew]

Unfortunately, I have no idea. It might be worth contacting matlab support over 
this. It seems like others (non-freesurfer) have had this issue, but there 
isn't much out there on how to resolve it.
Andrew


From: Iglesias Gonzalez, Juan E. 
Sent: Thursday, October 10, 2019 3:33 PM
To: Freesurfer support list
Cc: Hoopes, Andrew
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command

Bummer!
Andrew, any ideas on this?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Olamide Abiose 

Reply-To: Freesurfer support list 
Date: Thursday, 10 October 2019 at 15:14
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command


External Email - Use Caution
Thank you so much for your quick response. I saw this link and mentioned this 
to my server administrator, but he seemed to disagree that that was the source 
of the issue. There were definitely permissions issues when he first downloaded 
Matlab R2014b onto the server, but I think they've been resolved (I no longer 
have trouble accessing files and subdirectories within the MCRv84 folder). That 
being said, I haven't been able to find "checkRequiredMCRProducts," " 
deployrc," or "matlabrc," and I don't know where to begin to look. Please let 
me know if you have any suggestions!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Thursday, October 10, 2019 3:07 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command


Dear Ola,



This looks like a very ugly error but someone experienced something similar in 
the past and it turned out to be a permissions problem.

https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+FS6.0%5C-dev+%5C%28Jun27%2C+2018%5C%29+Hippocampal+subfield+Matlab+runtime+Java+error%22=newest=1



Can you please double check this is not your case?



Cheers,



/E



Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com





From:  on behalf of Olamide Abiose 

Reply-To: Freesurfer support list 
Date: Thursday, 10 October 2019 at 14:29
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Issues with segmentHA_T1.sh command



External Email - Use Caution

Hello,



I'm having great difficulty running the segmentHA_T1.sh command. I'm using the 
latest development version of Freesurfer and have downloaded Matlab R2014b. I 
get the following message when I try to run the command. Any advice/suggestions 
you can offer would be greatly appreciated!



Thank you very much.





#

#@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019

/usr/bin/time -o /dev/stdout

@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 
e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01

run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 
/mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 
0. 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz 
/opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left 
L-BFGS v21 /opt/freesurfer-dev/bin/ 0

--

Setting up environment variables

---

LD_LIBRARY_PATH is 
.:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::

Error using checkRequiredMCRProducts (line 25)

Java exception occurred:

java.lang.NullPointerException

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)

at 
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)



Error in deployrc (line 9)



Error in matlabrc (line 238)





Command exited with non-zero status 255

@#@FSTIME  2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 
84096 L 41.67 41.74 45.01

@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 41.42 41.68 44.90

Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux

Re: [Freesurfer] Contents of Freesurfer digest...

[Martin Reuter]

Hi David, 

nobody can really tell you what will happen if you use the software outside its 
tested use cases. 5mm thick slices, with tumor resection is not what it has 
been designed to work with. And as I said, gad enhanced also not. It might give 
you meaningful results or not. The only way to find out is to try it and make 
sure to carefully inspect the segmentation visually (in all three views). Don’t 
be fooled by the nice looking within-plane images. They are smooth averages 
across 5mm. Missing resolution in the 3rd direction will allow you do only 
detect large volume changes due to loss of sensitivity. How much you loose is 
unclear. 

Best, Martin


> On 10. Oct 2019, at 21:11, David Kamson  wrote:
> Martin, thank you for these comments. These are extremely valuable!
> 
> Although my patients had tumors, these are cured (this is why I have so few 
> of them…) and have no residual mass effect/deformity beyond biopsy tracks / 
> small resection cavities. Thus far, I was able to get pretty accurate looking 
> segmentations of deep nuclei on aseg. Segmentation issues were associated 
> with the surface structures (e.g.  dura/falx being misclassified as gray or 
> brain tissue adjacent to resection cavities are correctly classified as brain 
> but GM/WM often misclassified).  
> 
> I’m OK restricting the analysis to ventricular and deep GM volume, since what 
> I’m trying to measure is marked atrophy of these structure after chemotherapy 
> which I guess is in the range of 1-5%/year. The changes are mostly marked 
> enough to enable a visual qualitative analysis, however, quantitative data 
> would be clinically more helpful to clarify when, and how much change to 
> expect after treatment.
> 
> Do you think increasing the number of time points analyzed (I have 4-6 scans 
> per year for each patient) could eliminate the noise from head 
> positioning/slicing as long as the volumetric trends remain consistent? 
> Again, the data would be normalized per individual and I would not use 
> absolute volume for any comparative analysis. 
> 
> Thank you again. This message board is of incredible value!
> 
> Best regards,
> David
> 
> 
> 
> 
>> --
>> 
>> Message: 1
>> Date: Wed, 09 Oct 2019 10:48:48 +0200
>> From: Martin Reuter > >
>> Subject: Re: [Freesurfer] Questions re slice thickness, aseg and
>> longitudinal analysis
>> To: Freesurfer support list > >
>> Message-ID:
>> <7a4d059cb5cb42f390e03f523677a3362d17cb81.ca...@nmr.mgh.harvard.edu 
>> >
>> Content-Type: text/plain; charset="UTF-8"
>> 
>> Hi David, 
>> 
>> I am not very optimistic:
>> 
>> 5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You
>> will certainly get something, but it can be very unreliable and
>> completely wrong. Especially longitudinally these thick slices will
>> induce large variance due to different head positioning (and different
>> slice angulations) in the scanner.
>> 
>> Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will
>> not work if tumor lesions are present. 
>> 
>> About your questions:
>> 
>> 1. Surfaces update the aseg, but if you are only interested in the
>> volumes, you can skip this expensive step (potentially at the cost of
>> slightly higher noise levels in your measurements).
>> 
>> 2. I think not (see above). 5mm is too low.
>> 
>> 3. Theoretically yes, but I have never tested if the scripts will do
>> it. You could run up to the aseg in the cross, then create base (up to
>> aseg) and then run the longs up to aseg. Not even sure you really need
>> the base aseg. You might be able to just run the initial base
>> registration step, obtain the transformations and median norm.mgz
>> image, could be sufficient for the long runs. 
>> 
>> 4. No. Gad images won't work. 
>> 
>> Best, Martin
>> 
>> 
>>>External Email - Use Caution
>>> Freesurfers,
>>> 
>>> First of all, I'd like to express my gratitude to the community for
>>> the support that keeps researchers like myself afloat!
>>> 
>>> 
>>> I have a unique set of oncology patients that I want to evaluate for
>>> brain atrophy in a retrospective longitudinal analysis.
>>> I was thinking about using Aseg.auto results to assess longitudinal
>>> volume changes, but before I invest all the time I wanted to check
>>> with the community whether this makes any sense at all:
>>> 
>>> The dataset that looks like this:
>>> - 22 patients (no control dataset [yet])
>>> - 10-25 MRIs per patient acquired over 2-8 years in relatively
>>> uniform intervals
>>> - Patients had most of their scans on the same scanner, but
>>> scanners differed widely between patients
>>> - All patients have axial T1 post gadolinium scans of 1x1x5mm
>>> resolution (3D acquisition available in <10%)
>>> - About 80% of scans have an axial 

Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Rosalia Dacosta Aguayo]

External Email - Use Caution

You are really the boss Dr. Iglesias!!

Happy to know Ola is in expert hands :)

Rosalia


El jue., 10 oct. 2019 15:35, Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> escribió:

> Bummer!
>
> Andrew, any ideas on this?
>
> Cheers,
>
> /E
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
> *From: * on behalf of Olamide
> Abiose 
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 10 October 2019 at 15:14
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Issues with segmentHA_T1.sh command
>
>
>
> *External Email - Use Caution*
>
> Thank you so much for your quick response. I saw this link and mentioned
> this to my server administrator, but he seemed to disagree that that was
> the source of the issue. There were definitely permissions issues when he
> first downloaded Matlab R2014b onto the server, but I think they've been
> resolved (I no longer have trouble accessing files and subdirectories
> within the MCRv84 folder). That being said, I haven't been able to find 
> "checkRequiredMCRProducts,"
> " deployrc," or "matlabrc," and I don't know where to begin to look. Please
> let me know if you have any suggestions!
> --
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez,
> Juan E. 
> *Sent:* Thursday, October 10, 2019 3:07 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Issues with segmentHA_T1.sh command
>
>
>
> Dear Ola,
>
>
>
> This looks like a very ugly error but someone experienced something
> similar in the past and it turned out to be a permissions problem.
>
>
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+FS6.0%5C-dev+%5C%28Jun27%2C+2018%5C%29+Hippocampal+subfield+Matlab+runtime+Java+error%22=newest=1
>
>
>
> Can you please double check this is not your case?
>
>
>
> Cheers,
>
>
>
> /E
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
> *From: * on behalf of Olamide
> Abiose 
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 10 October 2019 at 14:29
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
> *Subject: *[Freesurfer] Issues with segmentHA_T1.sh command
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I'm having great difficulty running the segmentHA_T1.sh command. I'm using
> the latest development version of Freesurfer and have downloaded Matlab
> R2014b. I get the following message when I try to run the command. Any
> advice/suggestions you can offer would be greatly appreciated!
>
>
>
> Thank you very much.
>
>
>
>
>
> #
>
> #@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019
>
> /usr/bin/time -o /dev/stdout
>
> @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh
> N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67
> 41.74 45.01
>
> run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/
> PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice
> 0.
> /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz
> /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz
> /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05
> left L-BFGS v21 /opt/freesurfer-dev/bin/ 0
>
> --
>
> Setting up environment variables
>
> ---
>
> LD_LIBRARY_PATH is
> .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
>
> Error using checkRequiredMCRProducts (line 25)
>
> Java exception occurred:
>
> java.lang.NullPointerException
>
> at
> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
>
> at
> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
>
> at
> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
>
> at
> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
>
> at
> com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
>
>
>
> Error in deployrc (line 9)
>
>
>
> Error in matlabrc (line 238)
>
>
>
>
>
> Command exited with non-zero status 255
>
> @#@FSTIME  2019:10:09:17:49:49
> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P
> 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01
>
> @#@FSLOADPOST 2019:10:09:17:50:15
> 

Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Iglesias Gonzalez, Juan E.]

Bummer!
Andrew, any ideas on this?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Olamide Abiose 

Reply-To: Freesurfer support list 
Date: Thursday, 10 October 2019 at 15:14
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command


External Email - Use Caution
Thank you so much for your quick response. I saw this link and mentioned this 
to my server administrator, but he seemed to disagree that that was the source 
of the issue. There were definitely permissions issues when he first downloaded 
Matlab R2014b onto the server, but I think they've been resolved (I no longer 
have trouble accessing files and subdirectories within the MCRv84 folder). That 
being said, I haven't been able to find "checkRequiredMCRProducts," " 
deployrc," or "matlabrc," and I don't know where to begin to look. Please let 
me know if you have any suggestions!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Thursday, October 10, 2019 3:07 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command


Dear Ola,



This looks like a very ugly error but someone experienced something similar in 
the past and it turned out to be a permissions problem.

https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+FS6.0%5C-dev+%5C%28Jun27%2C+2018%5C%29+Hippocampal+subfield+Matlab+runtime+Java+error%22=newest=1



Can you please double check this is not your case?



Cheers,



/E



Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com





From:  on behalf of Olamide Abiose 

Reply-To: Freesurfer support list 
Date: Thursday, 10 October 2019 at 14:29
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Issues with segmentHA_T1.sh command



External Email - Use Caution

Hello,



I'm having great difficulty running the segmentHA_T1.sh command. I'm using the 
latest development version of Freesurfer and have downloaded Matlab R2014b. I 
get the following message when I try to run the command. Any advice/suggestions 
you can offer would be greatly appreciated!



Thank you very much.





#

#@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019

/usr/bin/time -o /dev/stdout

@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 
e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01

run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 
/mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 
0. 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz 
/opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left 
L-BFGS v21 /opt/freesurfer-dev/bin/ 0

--

Setting up environment variables

---

LD_LIBRARY_PATH is 
.:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::

Error using checkRequiredMCRProducts (line 25)

Java exception occurred:

java.lang.NullPointerException

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)

at 
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)



Error in deployrc (line 9)



Error in matlabrc (line 238)





Command exited with non-zero status 255

@#@FSTIME  2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 
84096 L 41.67 41.74 45.01

@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 41.42 41.68 44.90

Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux



T1 hippocampal subfields exited with ERRORS at Wed Oct  9 17:50:15 PDT 2019


___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Olamide Abiose]

External Email - Use Caution

Thank you so much for your quick response. I saw this link and mentioned this 
to my server administrator, but he seemed to disagree that that was the source 
of the issue. There were definitely permissions issues when he first downloaded 
Matlab R2014b onto the server, but I think they've been resolved (I no longer 
have trouble accessing files and subdirectories within the MCRv84 folder). That 
being said, I haven't been able to find "checkRequiredMCRProducts," " 
deployrc," or "matlabrc," and I don't know where to begin to look. Please let 
me know if you have any suggestions!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Thursday, October 10, 2019 3:07 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command


Dear Ola,



This looks like a very ugly error but someone experienced something similar in 
the past and it turned out to be a permissions problem.

https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+FS6.0%5C-dev+%5C%28Jun27%2C+2018%5C%29+Hippocampal+subfield+Matlab+runtime+Java+error%22=newest=1



Can you please double check this is not your case?



Cheers,



/E



Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com





From:  on behalf of Olamide Abiose 

Reply-To: Freesurfer support list 
Date: Thursday, 10 October 2019 at 14:29
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Issues with segmentHA_T1.sh command



External Email - Use Caution

Hello,



I'm having great difficulty running the segmentHA_T1.sh command. I'm using the 
latest development version of Freesurfer and have downloaded Matlab R2014b. I 
get the following message when I try to run the command. Any advice/suggestions 
you can offer would be greatly appreciated!



Thank you very much.





#

#@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019

/usr/bin/time -o /dev/stdout

@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 
e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01

run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 
/mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 
0. 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz 
/opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left 
L-BFGS v21 /opt/freesurfer-dev/bin/ 0

--

Setting up environment variables

---

LD_LIBRARY_PATH is 
.:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::

Error using checkRequiredMCRProducts (line 25)

Java exception occurred:

java.lang.NullPointerException

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)

at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)

at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)

at 
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)



Error in deployrc (line 9)



Error in matlabrc (line 238)





Command exited with non-zero status 255

@#@FSTIME  2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 
84096 L 41.67 41.74 45.01

@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 41.42 41.68 44.90

Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux



T1 hippocampal subfields exited with ERRORS at Wed Oct  9 17:50:15 PDT 2019


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Contents of Freesurfer digest...

[David Kamson]

External Email - Use Caution

Martin, thank you for these comments. These are extremely valuable!

Although my patients had tumors, these are cured (this is why I have so few of 
them…) and have no residual mass effect/deformity beyond biopsy tracks / small 
resection cavities. Thus far, I was able to get pretty accurate looking 
segmentations of deep nuclei on aseg. Segmentation issues were associated with 
the surface structures (e.g.  dura/falx being misclassified as gray or brain 
tissue adjacent to resection cavities are correctly classified as brain but 
GM/WM often misclassified).

I’m OK restricting the analysis to ventricular and deep GM volume, since what 
I’m trying to measure is marked atrophy of these structure after chemotherapy 
which I guess is in the range of 1-5%/year. The changes are mostly marked 
enough to enable a visual qualitative analysis, however, quantitative data 
would be clinically more helpful to clarify when, and how much change to expect 
after treatment.

Do you think increasing the number of time points analyzed (I have 4-6 scans 
per year for each patient) could eliminate the noise from head 
positioning/slicing as long as the volumetric trends remain consistent? Again, 
the data would be normalized per individual and I would not use absolute volume 
for any comparative analysis.

Thank you again. This message board is of incredible value!

Best regards,
David




--

Message: 1
Date: Wed, 09 Oct 2019 10:48:48 +0200
From: Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Questions re slice thickness, aseg and
longitudinal analysis
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<7a4d059cb5cb42f390e03f523677a3362d17cb81.ca...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="UTF-8"

Hi David,

I am not very optimistic:

5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You
will certainly get something, but it can be very unreliable and
completely wrong. Especially longitudinally these thick slices will
induce large variance due to different head positioning (and different
slice angulations) in the scanner.

Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will
not work if tumor lesions are present.

About your questions:

1. Surfaces update the aseg, but if you are only interested in the
volumes, you can skip this expensive step (potentially at the cost of
slightly higher noise levels in your measurements).

2. I think not (see above). 5mm is too low.

3. Theoretically yes, but I have never tested if the scripts will do
it. You could run up to the aseg in the cross, then create base (up to
aseg) and then run the longs up to aseg. Not even sure you really need
the base aseg. You might be able to just run the initial base
registration step, obtain the transformations and median norm.mgz
image, could be sufficient for the long runs.

4. No. Gad images won't work.

Best, Martin


   External Email - Use Caution
Freesurfers,

First of all, I'd like to express my gratitude to the community for
the support that keeps researchers like myself afloat!


I have a unique set of oncology patients that I want to evaluate for
brain atrophy in a retrospective longitudinal analysis.
I was thinking about using Aseg.auto results to assess longitudinal
volume changes, but before I invest all the time I wanted to check
with the community whether this makes any sense at all:

The dataset that looks like this:
- 22 patients (no control dataset [yet])
- 10-25 MRIs per patient acquired over 2-8 years in relatively
uniform intervals
- Patients had most of their scans on the same scanner, but
scanners differed widely between patients
- All patients have axial T1 post gadolinium scans of 1x1x5mm
resolution (3D acquisition available in <10%)
- About 80% of scans have an axial pre-contrast T1 sequence
- All scans are skullstripped (third party algorithm)

I'm looking for crude changes, no subtleties; volumes of interest
are:
- Whole brain volume
- White matter volume
- Ventricular volume (mainly lateral ventricle)
- Subcortical gray matter volume (whole thalamus most importantly)

I ran a few test analyses and to my surprise I was able to generate
pretty acceptable surfaces, however, topology fixing took about 24H
per scan, and I feel aseg.auto contained all the volumetric data I
was really interested in.

My concrete questions are:
1) Does the full autorecon pipeline affect Aseg.auto? If there is no
benefit, I could reduce the per scan analysis time from 28 hours to
1-2 h.
2) Would this low-resolution dataset be accepted by reviewers if used
for Aseg? Should I do any quantitative validation beyond a visual
quality analysis of Aseg?
3) Can I perform a longitudinal analysis only for the Aseg results?
4) Is it OK to use T1-gad images for the 

Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Iglesias Gonzalez, Juan E.]

Dear Ola,

This looks like a very ugly error but someone experienced something similar in 
the past and it turned out to be a permissions problem.
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+FS6.0%5C-dev+%5C%28Jun27%2C+2018%5C%29+Hippocampal+subfield+Matlab+runtime+Java+error%22=newest=1

Can you please double check this is not your case?

Cheers,

/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Olamide Abiose 

Reply-To: Freesurfer support list 
Date: Thursday, 10 October 2019 at 14:29
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Issues with segmentHA_T1.sh command


External Email - Use Caution
Hello,

I'm having great difficulty running the segmentHA_T1.sh command. I'm using the 
latest development version of Freesurfer and have downloaded Matlab R2014b. I 
get the following message when I try to run the command. Any advice/suggestions 
you can offer would be greatly appreciated!

Thank you very much.


#
#@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019
/usr/bin/time -o /dev/stdout
@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 
e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01
run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 
/mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 
0. 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz 
/opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left 
L-BFGS v21 /opt/freesurfer-dev/bin/ 0
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
Error using checkRequiredMCRProducts (line 25)
Java exception occurred:
java.lang.NullPointerException
at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
at 
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)

Error in deployrc (line 9)

Error in matlabrc (line 238)


Command exited with non-zero status 255
@#@FSTIME  2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 
84096 L 41.67 41.74 45.01
@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 41.42 41.68 44.90
Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Wed Oct  9 17:50:15 PDT 2019

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Rosalia Dacosta Aguayo]

External Email - Use Caution

I see, in that case, you should ask directly to Dr Eugenio Iglesias as he
is the one who created this script.

His last known email is: e.igles...@ucl.ac.uk

I am sure he will answer you as soon as possible, but if you see that there
is no answer. Then send it to the list cc to him as well. And mention his
name in your email so he will take your email quickly.

Best Wishes,
Rosalia



On Thu, Oct 10, 2019 at 8:49 PM Olamide Abiose  wrote:

> External Email - Use Caution
>
> Okay, here it is. I just want to stress that it's not my script, but the
> amygdala subfield module released by Freesurfer (
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
> I don't have permission to directly edit it, but please let me know if I'm
> misunderstanding your request, or if you'd like further clarification.
>
> Thanks again.
>
>
> --
> #! /bin/tcsh -f
>
> set tcsh61706 = (`tcsh --version | grep "6\.17\.06"`)
> if ("$tcsh61706" != "") then
>   echo ""
>   echo "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!"
>   echo ""
>   # workaround to force expected behavior:
>   set anyerror
> endif
>
> # check MCR installation
> checkMCR.sh
> if ($status) then
> exit 1
> endif
>
>
> # If no arguments given
> if( $#argv == 0 || $#argv > 2) then
>   echo " "
>   echo "Usage: "
>   echo " "
>   echo "   segmentHA_T1.sh SUBJECT_ID [SUBJECT_DIR]"
>   echo " "
>   echo "Or, for help"
>   echo " "
>   echo "   segmentHA_T1.sh --help"
>   echo " "
>   exit 1
> endif
>
> # If requesting help
> if( $1 == "--help") then
>   echo " "
>   echo "SEGMENTATION OF HIPPOCAMPAL SUBFIELDS AND NUCLEI OF THE AMYGDALA
> (T1)"
>   echo " "
>   echo "Use this script to segment the hippocampal subfields and nuclei of
> the amygdala"
>   echo "from the main T1 scan used in the recon-all stream. It supports
> standard (1mm)"
>   echo "and high resolution T1 scans."
>   echo " "
>   echo "To use this module, you first need to process the input scan with
> the main "
>   echo "FreeSurfer pipeline (recon-all). If you want to analyze
> high-resolution scans"
>   echo "(i.e., voxel size smaller than 1mm) at their native resolution,
> they must be"
>   echo "processed with the recon-all flag -cm. Then, you can run the
> following command"
>   echo "to obtain the segmentation: "
>   echo " "
>   echo "   segmentHA_T1.sh SUBJECT_ID [SUBJECT_DIR]"
>   echo " "
>   echo "   (the argument [SUBJECT_DIR] is only necessary if the"
>   echo "environment variable SUBJECTS_DIR has not been set"
>   echo "or if you want to override it)"
>   echo " "
>   echo "The segmentation method is described in [1], and the atlases are
> described in [1]"
>   echo "(hippocampus) and [2] (amygdala):"
>   echo " "
>   echo "See further information, including how to visualize the results,
> at:"
>   echo " "
>   echo "
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
> "
>   echo " "
>   echo "[1] Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M.,
> Player, A., Wright,"
>   echo "M., Roy, N., Frosch, M.P., McKee, A.C., Wald, L.L., Fischl, B.,
> and Van Leemput, K.,"
>   echo "A computational atlas of the hippocampal formation using ex vivo,
> ultra-high resolution"
>   echo "MRI: Application to adaptive segmentation of in vivo MRI.
> Neuroimage 115, 2015, 117-137."
>   echo "http://dx.doi.org/10.1016/j.neuroimage.2015.04.042;
>   echo " "
>   echo "[2] Saygin, Z.M. & Kliemann, D. (joint 1st authors), Iglesias,
> J.E., van der Kouwe, A.J.W.,"
>   echo "Boyd, E., Reuter, M., Stevens, A., Van Leemput, K., McKee, A.,
> Frosch, M.P., Fischl, B.,"
>   echo "and Augustinack, J.C., High-resolution magnetic resonance imaging
> reveals nuclei of the"
>   echo "human amygdala: manual segmentation to automatic atlas. Neuroimage
> 155, 2017, 370-382."
>   echo "http://doi.org/10.1016/j.neuroimage.2017.04.046;
>   echo " "
>   exit 0
> endif
>
> # Error if SUBJECTS_DIR (the environment variable) does not exist
> if ($#argv == 1) then
>   if (! $?SUBJECTS_DIR)  then
> echo " "
> echo "SUBJECTS_DIR variable does not exist"
> echo "Please define it or provide subjects directory as second input"
> echo " "
> exit 1
>   endif
> endif
>
> # Error if SUBJECTS_DIR (the environemnt variable) is empty
> if ($#argv == 1) then
>   if ( $SUBJECTS_DIR == "" ) then
> echo " "
> echo "SUBJECTS_DIR variable is empty"
> echo "Please redefine it or provide subjects directory as second input"
> echo " "
> exit 1
>   endif
> endif
>
> # If SUBJECTS_DIR is provided, just set it
> if ($#argv == 2) then
>   set SUBJECTS_DIR = $2
> endif
>
> # Set name of subject
> set 

Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Olamide Abiose]

External Email - Use Caution

Okay, here it is. I just want to stress that it's not my script, but the 
amygdala subfield module released by Freesurfer 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
 I don't have permission to directly edit it, but please let me know if I'm 
misunderstanding your request, or if you'd like further clarification.

Thanks again.

--
#! /bin/tcsh -f

set tcsh61706 = (`tcsh --version | grep "6\.17\.06"`)
if ("$tcsh61706" != "") then
  echo ""
  echo "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!"
  echo ""
  # workaround to force expected behavior:
  set anyerror
endif

# check MCR installation
checkMCR.sh
if ($status) then
exit 1
endif


# If no arguments given
if( $#argv == 0 || $#argv > 2) then
  echo " "
  echo "Usage: "
  echo " "
  echo "   segmentHA_T1.sh SUBJECT_ID [SUBJECT_DIR]"
  echo " "
  echo "Or, for help"
  echo " "
  echo "   segmentHA_T1.sh --help"
  echo " "
  exit 1
endif

# If requesting help
if( $1 == "--help") then
  echo " "
  echo "SEGMENTATION OF HIPPOCAMPAL SUBFIELDS AND NUCLEI OF THE AMYGDALA (T1)"
  echo " "
  echo "Use this script to segment the hippocampal subfields and nuclei of the 
amygdala"
  echo "from the main T1 scan used in the recon-all stream. It supports 
standard (1mm)"
  echo "and high resolution T1 scans."
  echo " "
  echo "To use this module, you first need to process the input scan with the 
main "
  echo "FreeSurfer pipeline (recon-all). If you want to analyze high-resolution 
scans"
  echo "(i.e., voxel size smaller than 1mm) at their native resolution, they 
must be"
  echo "processed with the recon-all flag -cm. Then, you can run the following 
command"
  echo "to obtain the segmentation: "
  echo " "
  echo "   segmentHA_T1.sh SUBJECT_ID [SUBJECT_DIR]"
  echo " "
  echo "   (the argument [SUBJECT_DIR] is only necessary if the"
  echo "environment variable SUBJECTS_DIR has not been set"
  echo "or if you want to override it)"
  echo " "
  echo "The segmentation method is described in [1], and the atlases are 
described in [1]"
  echo "(hippocampus) and [2] (amygdala):"
  echo " "
  echo "See further information, including how to visualize the results, at:"
  echo " "
  echo 
"https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala;
  echo " "
  echo "[1] Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M., 
Player, A., Wright,"
  echo "M., Roy, N., Frosch, M.P., McKee, A.C., Wald, L.L., Fischl, B., and Van 
Leemput, K.,"
  echo "A computational atlas of the hippocampal formation using ex vivo, 
ultra-high resolution"
  echo "MRI: Application to adaptive segmentation of in vivo MRI.  Neuroimage 
115, 2015, 117-137."
  echo "http://dx.doi.org/10.1016/j.neuroimage.2015.04.042;
  echo " "
  echo "[2] Saygin, Z.M. & Kliemann, D. (joint 1st authors), Iglesias, J.E., 
van der Kouwe, A.J.W.,"
  echo "Boyd, E., Reuter, M., Stevens, A., Van Leemput, K., McKee, A., Frosch, 
M.P., Fischl, B.,"
  echo "and Augustinack, J.C., High-resolution magnetic resonance imaging 
reveals nuclei of the"
  echo "human amygdala: manual segmentation to automatic atlas. Neuroimage 155, 
2017, 370-382."
  echo "http://doi.org/10.1016/j.neuroimage.2017.04.046;
  echo " "
  exit 0
endif

# Error if SUBJECTS_DIR (the environment variable) does not exist
if ($#argv == 1) then
  if (! $?SUBJECTS_DIR)  then
echo " "
echo "SUBJECTS_DIR variable does not exist"
echo "Please define it or provide subjects directory as second input"
echo " "
exit 1
  endif
endif

# Error if SUBJECTS_DIR (the environemnt variable) is empty
if ($#argv == 1) then
  if ( $SUBJECTS_DIR == "" ) then
echo " "
echo "SUBJECTS_DIR variable is empty"
echo "Please redefine it or provide subjects directory as second input"
echo " "
exit 1
  endif
endif

# If SUBJECTS_DIR is provided, just set it
if ($#argv == 2) then
  set SUBJECTS_DIR = $2
endif

# Set name of subject
set SUBJECTNAME = $1

# Error if subject directory does not exist
if (! -d $SUBJECTS_DIR ) then
  echo " "
  echo "Subjects directory:"
  echo "   $SUBJECTS_DIR"
  echo "does not exist"
  echo " "
  exit 1
endif

# Error if directory of specific subject does not exist
if (! -d $SUBJECTS_DIR/$SUBJECTNAME ) then
  echo " "
  echo "Directory of subject to process:"
  echo "   $SUBJECTS_DIR/$SUBJECTNAME"
  echo "does not exist"
  echo " "
  exit 1
endif

# Error if subject not processed (far enough)
if (! -e ${SUBJECTS_DIR}/${SUBJECTNAME}/mri/wmparc.mgz || \
! -e ${SUBJECTS_DIR}/${SUBJECTNAME}/mri/norm.mgz || \
! -e ${SUBJECTS_DIR}/${SUBJECTNAME}/mri/transforms/talairach.xfm ) then
  echo " "
  echo "Cannot find 

Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi,

Yes, otherwise there is no way to debug the lines in your script.

Best,
Rosalia

El jue., 10 oct. 2019 14:41, Olamide Abiose  escribió:

> External Email - Use Caution
>
> Hi Rosalia,
>
> I'm running this as a command line argument, because I'm only testing one
> subject. Are you asking for the segmentHA_T1.sh script?
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta
> Aguayo 
> *Sent:* Thursday, October 10, 2019 2:34 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Issues with segmentHA_T1.sh command
>
>
> External Email - Use Caution
>
> Hi Olamide,
>
> How to check your line errors without the bash script you are using?
> Could you at least send the .sh script?
>
> Best regards,
> Rosalia
>
> On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose 
> wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I'm having great difficulty running the segmentHA_T1.sh command. I'm using
> the latest development version of Freesurfer and have downloaded Matlab
> R2014b. I get the following message when I try to run the command. Any
> advice/suggestions you can offer would be greatly appreciated!
>
> Thank you very much.
>
>
> #
> #@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019
> /usr/bin/time -o /dev/stdout
> @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh
> N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67
> 41.74 45.01
> run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/
> PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice
> 0.
> /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz
> /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz
> /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05
> left L-BFGS v21 /opt/freesurfer-dev/bin/ 0
> --
> Setting up environment variables
> ---
> LD_LIBRARY_PATH is
> .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
> Error using checkRequiredMCRProducts (line 25)
> Java exception occurred:
> java.lang.NullPointerException
> at
> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
> at
> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
> at
> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
> at
> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
> at
> com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
>
> Error in deployrc (line 9)
>
> Error in matlabrc (line 238)
>
>
> Command exited with non-zero status 255
> @#@FSTIME  2019:10:09:17:49:49
> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P
> 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01
> @#@FSLOADPOST 2019:10:09:17:50:15
> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90
> Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019
> x86_64 x86_64 x86_64 GNU/Linux
>
> T1 hippocampal subfields exited with ERRORS at Wed Oct  9 17:50:15 PDT 2019
>
> ___
> 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] Issues with segmentHA_T1.sh command

[Olamide Abiose]

External Email - Use Caution

Hi Rosalia,

I'm running this as a command line argument, because I'm only testing one 
subject. Are you asking for the segmentHA_T1.sh script?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rosalia Dacosta Aguayo 

Sent: Thursday, October 10, 2019 2:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command


External Email - Use Caution

Hi Olamide,

How to check your line errors without the bash script you are using?
Could you at least send the .sh script?

Best regards,
Rosalia

On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose 
mailto:oabi...@stanford.edu>> wrote:

External Email - Use Caution

Hello,

I'm having great difficulty running the segmentHA_T1.sh command. I'm using the 
latest development version of Freesurfer and have downloaded Matlab R2014b. I 
get the following message when I try to run the command. Any advice/suggestions 
you can offer would be greatly appreciated!

Thank you very much.


#
#@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019
/usr/bin/time -o /dev/stdout
@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 
e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01
run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 
/mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 
0. 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz 
/opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left 
L-BFGS v21 /opt/freesurfer-dev/bin/ 0
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
Error using checkRequiredMCRProducts (line 25)
Java exception occurred:
java.lang.NullPointerException
at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
at 
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)

Error in deployrc (line 9)

Error in matlabrc (line 238)


Command exited with non-zero status 255
@#@FSTIME  2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 
84096 L 41.67 41.74 45.01
@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 41.42 41.68 44.90
Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Wed Oct  9 17:50:15 PDT 2019

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Re: [Freesurfer] Issues with segmentHA_T1.sh command

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Olamide,

How to check your line errors without the bash script you are using?
Could you at least send the .sh script?

Best regards,
Rosalia

On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose  wrote:

> External Email - Use Caution
>
> Hello,
>
> I'm having great difficulty running the segmentHA_T1.sh command. I'm using
> the latest development version of Freesurfer and have downloaded Matlab
> R2014b. I get the following message when I try to run the command. Any
> advice/suggestions you can offer would be greatly appreciated!
>
> Thank you very much.
>
>
> #
> #@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019
> /usr/bin/time -o /dev/stdout
> @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh
> N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67
> 41.74 45.01
> run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/
> PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice
> 0.
> /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz
> /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz
> /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05
> left L-BFGS v21 /opt/freesurfer-dev/bin/ 0
> --
> Setting up environment variables
> ---
> LD_LIBRARY_PATH is
> .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
> Error using checkRequiredMCRProducts (line 25)
> Java exception occurred:
> java.lang.NullPointerException
> at
> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
> at
> com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
> at
> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
> at
> com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
> at
> com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
>
> Error in deployrc (line 9)
>
> Error in matlabrc (line 238)
>
>
> Command exited with non-zero status 255
> @#@FSTIME  2019:10:09:17:49:49
> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P
> 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01
> @#@FSLOADPOST 2019:10:09:17:50:15
> run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90
> Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019
> x86_64 x86_64 x86_64 GNU/Linux
>
> T1 hippocampal subfields exited with ERRORS at Wed Oct  9 17:50:15 PDT 2019
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Issues with segmentHA_T1.sh command

[Olamide Abiose]

External Email - Use Caution

Hello,

I'm having great difficulty running the segmentHA_T1.sh command. I'm using the 
latest development version of Freesurfer and have downloaded Matlab R2014b. I 
get the following message when I try to run the command. Any advice/suggestions 
you can offer would be greatly appreciated!

Thank you very much.


#
#@# Hippocampal Subfields processing (T1) left Wed Oct  9 17:49:49 PDT 2019
/usr/bin/time -o /dev/stdout
@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 
e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01
run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 
/mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 
0. 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz 
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz 
/opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left 
L-BFGS v21 /opt/freesurfer-dev/bin/ 0
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
Error using checkRequiredMCRProducts (line 25)
Java exception occurred:
java.lang.NullPointerException
at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
at 
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
at 
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
at 
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)

Error in deployrc (line 9)

Error in matlabrc (line 238)


Command exited with non-zero status 255
@#@FSTIME  2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 
13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 
84096 L 41.67 41.74 45.01
@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh 
N 13 41.42 41.68 44.90
Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 
x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Wed Oct  9 17:50:15 PDT 2019

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Re: [Freesurfer] TRACULA error - MRISread could not open file

[Yendiki, Anastasia]

It appears to be a bbregister error:
bbregister --s APOE.269 --init-fsl --dti --mov 
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/dwi.nii.gz --reg 
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/anatorig2diff.bbr.dat --fslmat 
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/diff2anatorig.bbr.mat

Make sure that SUBJECTS_DIR is correct in the config file. If the problem 
persists, please email about the bbregister problem separately and perhaps Doug 
can assist you. Note that I'll be traveling and may not be responding to email 
in the next 10 days.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Thursday, October 10, 2019 9:20 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA error - MRISread could not open file


External Email - Use Caution

Hello,

It isn't an error with recon-all, at least I don't think it is. Recon-all ran 
without error and the file that Tracula is trying to access seems to be where 
it is supposed to be. It seems like Tracula is having an issue opening the 
lh.white file. I just included the recon-all log for that subject to show that 
recon-all hadn't had any issues. Do you still think it would have to do with 
recon-all? It seems to have to do with the way Tracula is trying to read the 
file?

Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298


On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error" 
in the subject line if you want the developers of the structural stream to look 
into it.

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Daniel Callow mailto:ddcc2...@gmail.com>>
Sent: Thursday, October 10, 2019 9:01:25 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] TRACULA error - MRISread could not open file


External Email - Use Caution

Hello,

I am running tracula on some of my DTI data and have had no issues for most of 
my subjects. However, for one of them I get the following error after mri_segreg


MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open 
file

Loading mov

Extracting frame 0

Projecting LH Surfs

Loading lh.white surf

No such file or directory


It doesn't make sense that I am getting this error because when looking in that 
exact folder I see the following


[255a-280:freesurfer_pin/APOE.269/surf] amos% ls

lh.area lh.smoothwm.FI.crv  rh.area rh.smoothwm.FI.crv

lh.curv lh.smoothwm.H.crv   rh.curv rh.smoothwm.H.crv

lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders   rh.smoothwm.K.crv

lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull rh.smoothwm.K1.crv

lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labelsrh.smoothwm.K2.crv

lh.inflated lh.smoothwm.S.crv   rh.inflated rh.smoothwm.S.crv

lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H   rh.smoothwm.nofix

lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere

lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc

lh.orig lh.sulc rh.orig rh.white.H

lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K

lh.qsphere.nofixlh.white.K  rh.qsphere.nofixrh.white.preaparc

lh.smoothwm lh.white.preaparc   rh.smoothwm rh.white.preaparc.H

lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv  rh.white.preaparc.K

lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv


It looks like the file it can't open is there? I have attached the log file for 
recon-all and trac-all the subject in case it might help.


Thank you,

Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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[Freesurfer] fsaverage label into functional space

[Lauri Tuominen]

External Email - Use Caution

Dear FreeSurfers! 

I would like to confirm something before I proceed with my analyses. I think I 
am just confused again. 

I am doing resting state analysis using fsfast. I am trying to use a label 
defined in the fsaverage space as a seed using the fcseed-config & fcseed-sess 
commands. Now these commands say that the label should be in fuctional space, 
which I gather is the space of the f.nii. 

So in order to move the label into functional space I say:

mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o 
lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01  --hemi lh 
--temp ${projectdir}/${sessionj}/rest/001/f.nii --fill-ribbon --reg 
${projectdir}/${session}/rest/register.dof6.lta

To my surprise, the voxel size here corresponds to the anatomical (orig.mgz) 
but not the functional space (f.nii). To test this further I did: 

mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o 
lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01  --hemi lh 
--temp $SUBJECTS_DIR/$/${sessionj}/mri/orig.mgz --fill-ribbon --reg 
${projectdir}/${session}/rest/register.dof6.lta

And I get exactly the same ROI in the volume. 

So just to confirm, is this what I want for the fcseed -commands?

Thank you so much again! 

Lauri Tuominen

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[Freesurfer] Cerebellar edits to correct aseg

[Zeng,Victor (BIDMC - Psychiatry)]

Hi,


according to this page: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview ,  
there is a separate protocol to correct cerebellar errors with rois such as the 
lingual gyrus, fusiform and etc specially the creation of the 
brain.finalsurfs.manedit file. I have a few questions about this step:


I'm assuming that the recon-2, if it detects a brain.finalsurfs.manedit, it 
makes a mask out of it, and applies it to brain.finalsurfs? The potential 
conflict I see here if that's not the case is this scenario: I'm doing all the 
manual edits for the brainmask, re-run recon23, then I create the 
brain.finalsurfs.manedit and correct the cerebellum, running the recon-all 
-autorecon-pial. Then I realize that there are still recon errors, and I edit 
the brainmask again. Would this second instance of editing the brainmask be 
negated by the fact that the brain.finalsurfs.manedit file doesn't have these 
edits?


Also, generally, is it okay to do other sort of edits (e.g removing the blood 
vessel between the cerebral cortex and the cerebellum) @ the 
brain.finalsurfs.manedit, rather than the brainmask.mgz?


best


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
ph: 617 754 1237
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[Freesurfer] Notice on freesurfer list archives

[Hoopes, Andrew]

Hi all,

Our primary archive for all posts to the mailing list can be found at:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu

And we've now disabled the public 'pipermail' archives, which include anything 
under:

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer

If you come across any broken links pointing to the above, please let us know.

best
Andrew

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Re: [Freesurfer] make_average_subject error

[Hoopes, Andrew]

Hi Maxine,

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ contains 
executables and a README file that details how you can patch your freesurfer 
install to fix this issue.

best
Andrew


From:  on behalf of Maxime Perron 

Reply-To: FS Help 
Date: Friday, September 6, 2019 at 5:08 PM
To: FS Help 
Subject: Re: [Freesurfer] make_average_subject error


External Email - Use Caution

​Hi Douglas,



I'm sorry for the misunderstanding! Thanks for the command.



I attached the mas.log.



Cheers,

Maxime

​




De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Greve, Douglas N.,Ph.D. 

Envoyé : 6 septembre 2019 10:30
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] make_average_subject error

That is the recon-all.log file. What I want is the terminal output from 
make_average_subject
You can capture it with
make_average_subject [your arguments] |& tee mas.log


On 9/4/2019 9:16 PM, Maxime Perron wrote:

External Email - Use Caution



Good evening Greve,



Thanks for your quick answer.



I attached the file containing the output.



Best,

Maxime



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On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D. 
 wrote:

Can you send the full text of the terminal output?



On 9/4/19 10:44 AM, Maxime Perron wrote:

External Email - Use Caution



Hi Greve,



The exact script is the following :





setenv SUBJECTS_DIR 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data



make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" 
"Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" 
"Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" 
"Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" 
"Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" 
"Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" 
"Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" 
"Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" 
"Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" 
"Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" 
"Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" 
"Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" 
"Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" 
"Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" 
"Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" 
"Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" 
"Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" 
"Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" 
"Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72



cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72

mkdir ori



cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72

@SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72



_



BrainaverageN72 is the output name.



Thanks,

Maxime Perron



De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 de la part de Greve, Douglas N.,Ph.D. 


Envoyé : 4 septembre 2019 10:37

À : freesurfer@nmr.mgh.harvard.edu

Objet : Re: [Freesurfer] make_average_subject error



Is BrainaverageN72 in the subjects list?



On 9/3/19 12:39 PM, Maxime Perron wrote:

External Email - Use Caution



​Dear Freesurfer Experts,





I have the following issue when running the make_average_subject command (



make_average_subject --subjects (Subjid) --out BrainaverageN72) :





Building hash of lh white



Building hash of lh pial



Building hash of rh white



Building hash of rh pial



Loading aseg from

/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz

ASeg Vox2RAS: ---

-1.0   0.0   0.0   128.0;

 0.0   0.0   1.0  -128.0;

 0.0  -1.0   0.0   128.0;

 0.0   0.0   0.0   1.0;

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

-



Labeling Slice

relabeling unlikely voxels in interior of white matter

Segmentation fault

Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun

Jun  2 20:31:42 

Re: [Freesurfer] Error in running make_average_subject

[Hoopes, Andrew]

Hi Himanshu,

Our pub disk went down a while ago and we lost the 6.0 patch files, but I've 
just updated that link with the necessary executables and README file. 
Following the readme instructions should fix your issue.

best
Andrew

From:  on behalf of Himanshu Aggarwal 

Reply-To: FS Help 
Date: Sunday, September 15, 2019 at 12:25 PM
To: FS Help 
Subject: [Freesurfer] Error in running make_average_subject


External Email - Use Caution

Hello Freesurfer Developers

I am trying to create an average subject for 20 subjects using the function 
make_average_subject. But I keep running into a segmentation fault. I have 
attached the recon-all.log file.

I found a few other posts about the same problem which direct the users to the 
following patch:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

But this patch does not have a readme file which can instruct the users about 
the steps that need to be followed to get rid of this bug. However, I have 
replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) 
with the files given in this patch directory. But the problem still persists. 
Kindly provide the steps that need to be followed to make use of this patch 
properly.

Regards

Himanshu

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[Freesurfer] Brainhack Global 2019: Call for Local Event Sites and Participation

[brainhack org]

External Email - Use Caution

Dear colleagues,


*apologise for cross posting*


Brainhack Global 2019 is collecting registrations for hosting sites! The
event will be run globally, on November 13-17, to share ideas and
experiences with colleagues across diverse disciplines and institutes.


Don’t forget that you are the designer of your own event! You can run your
hackathon around a theme that your institute is working on, hold a train
track to share the expertise among your colleagues or broadcast all around
the world, propose your own projects to run collaboratively and make them
heard across the globe, or work on local proceedings and guidelines that
would facilitate open and transparent scientific research for the local and
global neuroscience community.


Brainhack Global 2019 team is ready to help in hosting local events. Please
check our website for more information and FAQs, and our Github repository
for guidelines and materials that we provide. If you are interested in
running a Brainhack, please fill the form in the Brainhack Global 2019
website! If you are planning to participate in an event, please check out
the 2019 event hosts registered with us so far from the Brainhack Global
2019 website.


http://brainhack.org/global2019/


Read our FAQs!  http://www.brainhack.org/global2019/#faq


Follow Brainhack Twitter!  https://twitter.com/brainhackorg


Join discussions on Brainhack Mattermost!

https://mattermost.brainhack.org/brainhack/channels/brainhack-global-2019


Important Dates

13 November 2019 Host confirmation

13-17 November 2019 Brainhack events


We look forward to having you all in this very exciting event!



The Brainhack Global 2019 Organizing Committee

Cameron Craddock, The University of Texas at Austin Dell Medical School,
Texas, USA

Pierre Bellec, Centre de Recherche de l'Institut Universitaire de Gériatrie
de Montréal, Montréal, Canada

Daniel Margulies, CNRS, Paris, France

Isil Poyraz Bilgin, The University of Reading, Reading, UK

Sofie Van Den Bossche, Ghent University, Ghent, Belgium

Damion Demeter, The University of Texas, Texas, USA

Anibal Sólon Heinsfeld, The University of Texas at Austin Dell Medical
School, Texas, USA

Peer Herholz, Montréal Neurological Institute & Hospital, McGill
University, Montréal, Canada

Jon Haitz Legarreta, Université de Sherbrooke, Sherbrooke, Canada
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[Freesurfer] Freesurfer 6 current state of submillimeter processing

[Daniel Westfall]

External Email - Use Caution

Hi Everyone,

I just wanted to double check the current state of processing T3
submillimeter data with Freesurfer 6. We have two studies: one with 0.9 mm
isotropic and the other with 0.8 mm isotropic. After doing some
investigating, I found that there is either the option to run recon-all
with the -hires flag (
https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon) or I found
that on the release notes for Freesurfer 6 there is a patch (
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/). I
would guess that the patch method is the most recent version that I should
use?

Thank you for the assistance.

Best,
Daniel
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Re: [Freesurfer] TRACULA error - MRISread could not open file

[Daniel Callow]

External Email - Use Caution

Hello,

It isn't an error with recon-all, at least I don't think it is. Recon-all
ran without error and the file that Tracula is trying to access seems to be
where it is supposed to be. It seems like Tracula is having an issue
opening the lh.white file. I just included the recon-all log for that
subject to show that recon-all hadn't had any issues. Do you still think it
would have to do with recon-all? It seems to have to do with the way
Tracula is trying to read the file?

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia 
wrote:

> Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula
> error" in the subject line if you want the developers of the structural
> stream to look into it.
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Daniel Callow <
> ddcc2...@gmail.com>
> *Sent:* Thursday, October 10, 2019 9:01:25 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] TRACULA error - MRISread could not open file
>
>
> External Email - Use Caution
>
> Hello,
>
> I am running tracula on some of my DTI data and have had no issues for
> most of my subjects. However, for one of them I get the following error
> after mri_segreg
>
> MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not
> open file
>
> Loading mov
>
> Extracting frame 0
>
> Projecting LH Surfs
>
> Loading lh.white surf
>
> No such file or directory
>
>
> It doesn't make sense that I am getting this error because when looking in
> that exact folder I see the following
>
>
> [255a-280:freesurfer_pin/APOE.269/surf] amos% ls
>
> lh.area lh.smoothwm.FI.crv  rh.area
> rh.smoothwm.FI.crv
>
> lh.curv lh.smoothwm.H.crv   rh.curv
> rh.smoothwm.H.crv
>
> lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders
> rh.smoothwm.K.crv
>
> lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull
> rh.smoothwm.K1.crv
>
> lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labels
> rh.smoothwm.K2.crv
>
> lh.inflated lh.smoothwm.S.crv   rh.inflated
> rh.smoothwm.S.crv
>
> lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H
> rh.smoothwm.nofix
>
> lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere
>
> lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc
>
> lh.orig lh.sulc rh.orig rh.white.H
>
> lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K
>
> lh.qsphere.nofixlh.white.K  rh.qsphere.nofix
> rh.white.preaparc
>
> lh.smoothwm lh.white.preaparc   rh.smoothwm
> rh.white.preaparc.H
>
> lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv
> rh.white.preaparc.K
>
> lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv
>
>
> It looks like the file it can't open is there? I have attached the log
> file for recon-all and trac-all the subject in case it might help.
>
>
> Thank you,
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
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Re: [Freesurfer] TRACULA error - MRISread could not open file

[Yendiki, Anastasia]

Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error" 
in the subject line if you want the developers of the structural stream to look 
into it.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Daniel Callow 

Sent: Thursday, October 10, 2019 9:01:25 AM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA error - MRISread could not open file


External Email - Use Caution

Hello,

I am running tracula on some of my DTI data and have had no issues for most of 
my subjects. However, for one of them I get the following error after mri_segreg


MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open 
file

Loading mov

Extracting frame 0

Projecting LH Surfs

Loading lh.white surf

No such file or directory


It doesn't make sense that I am getting this error because when looking in that 
exact folder I see the following


[255a-280:freesurfer_pin/APOE.269/surf] amos% ls

lh.area lh.smoothwm.FI.crv  rh.area rh.smoothwm.FI.crv

lh.curv lh.smoothwm.H.crv   rh.curv rh.smoothwm.H.crv

lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders   rh.smoothwm.K.crv

lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull rh.smoothwm.K1.crv

lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labelsrh.smoothwm.K2.crv

lh.inflated lh.smoothwm.S.crv   rh.inflated rh.smoothwm.S.crv

lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H   rh.smoothwm.nofix

lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere

lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc

lh.orig lh.sulc rh.orig rh.white.H

lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K

lh.qsphere.nofixlh.white.K  rh.qsphere.nofixrh.white.preaparc

lh.smoothwm lh.white.preaparc   rh.smoothwm rh.white.preaparc.H

lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv  rh.white.preaparc.K

lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv


It looks like the file it can't open is there? I have attached the log file for 
recon-all and trac-all the subject in case it might help.


Thank you,

Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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[Freesurfer] TRACULA error - MRISread could not open file

[Daniel Callow]

External Email - Use Caution

Hello,

I am running tracula on some of my DTI data and have had no issues for most
of my subjects. However, for one of them I get the following error after
mri_segreg

MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not
open file

Loading mov

Extracting frame 0

Projecting LH Surfs

Loading lh.white surf

No such file or directory


It doesn't make sense that I am getting this error because when looking in
that exact folder I see the following


[255a-280:freesurfer_pin/APOE.269/surf] amos% ls

lh.area lh.smoothwm.FI.crv  rh.area
rh.smoothwm.FI.crv

lh.curv lh.smoothwm.H.crv   rh.curv
rh.smoothwm.H.crv

lh.defect_borders   lh.smoothwm.K.crv   rh.defect_borders
rh.smoothwm.K.crv

lh.defect_chull lh.smoothwm.K1.crv  rh.defect_chull
rh.smoothwm.K1.crv

lh.defect_labelslh.smoothwm.K2.crv  rh.defect_labels
rh.smoothwm.K2.crv

lh.inflated lh.smoothwm.S.crv   rh.inflated
rh.smoothwm.S.crv

lh.inflated.H   lh.smoothwm.nofix   rh.inflated.H
rh.smoothwm.nofix

lh.inflated.K   lh.sphere   rh.inflated.K   rh.sphere

lh.inflated.nofix   lh.sphere.reg   rh.inflated.nofix   rh.sulc

lh.orig lh.sulc rh.orig rh.white.H

lh.orig.nofix   lh.white.H  rh.orig.nofix   rh.white.K

lh.qsphere.nofixlh.white.K  rh.qsphere.nofix
rh.white.preaparc

lh.smoothwm lh.white.preaparc   rh.smoothwm
rh.white.preaparc.H

lh.smoothwm.BE.crv  lh.white.preaparc.H rh.smoothwm.BE.crv
rh.white.preaparc.K

lh.smoothwm.C.crv   lh.white.preaparc.K rh.smoothwm.C.crv


It looks like the file it can't open is there? I have attached the log file
for recon-all and trac-all the subject in case it might help.


Thank you,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


recon-all-status.log
Description: Binary data


trac-all.error
Description: Binary data


trac-all.log
Description: Binary data
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[Freesurfer] PhD & Postdoc positions – computational modeling and real-time fMRI neurofeedback of language, bilingualism and dyslexia

[Narly Golestani]

External Email - Use Caution

PhD & Postdoc positions – computational modeling and real-time fMRI 
neurofeedback of language, bilingualism and dyslexia

PhD and Postdoc positions are available at the Brain and Language Lab 
(www.brainandlanguagelab.org) at the 
University of Geneva. The PhD position is for 3-4 years, and the postdoc 
position is for up to 4 years, and salary will be commensurate with experience. 
 Several projects will be done in collaborations with Maastricht University and 
with the University of Vienna.

Applicants should have a strong interest in human brain imaging, and in 
language function and dysfunction, and should have one of (or a combination of) 
the following profiles:

1. Candidates with a degree in Biomedical Engineering, Computational 
Neuroscience, or a related field, and with solid experience in computational 
modelling (i.e. encoding / decoding) of fMRI data, machine learning, statistics 
and programming. Projects will include extensions of our recent work on the 
neural encoding of acoustic information in speech sounds 
(https://www.ncbi.nlm.nih.gov/pubmed/31285622) to higher levels of language 
processing.

2. Candidates with a degree in Cognitive Neuroscience, Biomedical Engineering 
and/or Psychology, with solid experience in the acquisition and analysis of 
brain functional (and structural) imaging data. Projects will include real-time 
fMRI neurofeedback training studies, focusing on different levels/aspects of 
language learning.

Candidates for either position (depending on experience) will also have the 
opportunity to become involved in the analysis of data from a 7T myelin mapping 
(R1) study.

The positions are available immediately, and applications will be considered 
until the position is filled. Applicants should send me their CV, a statement 
of research interests, and the names and contact information for 2-3 
references, at narly.golest...@unige.ch.

-
Prof. Narly Golestani
Brain and Language Lab
Department of Psychology
Campus Biotech
9 Chemin des Mines,
1202 Genève
+41 22 379 53 52
http://www.brainandlanguagelab.org
https://twitter.com/brain_lang_lab
-

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[Freesurfer] FS dev install error at mri_surf2vol on mac

[fsbuild]

External Email - Use Caution

Hello Jonathan,



It could help to add -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON to the cmake 
command line to see what the compiler is doing when you run make and see the 
first instance of those errors, but 
clearly something is not right with the linker options..



You could also try downloading makefile.wiki from, 
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing

- and then rename it to makefile. This should go in the same 
subdirectory as your ./freesurfer folder as created by git.



The makefile has targets to fetch/update/setup everything from github, 
fetch the archive of 3rd party libs needed to build freesurfer, show you
 the cmake command it will run, run that cmake command, run the make command to 
compile 
the source, then do the install pass. You can see what the steps are if 
you type "make help". This works for me on Mac OS 
10.13.6 (High Sierra) with the native clang compilers. I also use a 
homebrew installation already on my Mac installed under /usr/local, 
though the makefile will try and set that up w/o actually installing it 
under /usr/local.



- R.



Jonathan DuBois wrote:

ld: warning: could not create compact unwind for _MatSetValuesLocal: 
stack subq instruction is too different from dwarf stack size




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