[Freesurfer] mri_fill unsuccessful in macaque

[Tello, Lawrence (NIH/NEI) [F]]

External Email - Use Caution

Hello,

I am trying to generate an inflated surface for a macaque brain, but mri_fill 
has stopped working for this subject. Below is my command line and output. I 
specify the corpus callosum and pons as well. Any suggestions?


mri_fill -CV 101 100 66 -PV 115 140 77 ./mri/wm/wm.nii.gz 
./mri/filled/filled.mgz
using voxel position (101, 100, 66) as corpus callosum seed point
using voxel position (115, 140, 77) as pons seed point
reading input volume...done.
searching for cutting planes...INFO: volume does not have linear_transform set 
nor lta is given by option.-xform.
INFO: use identity matrix as the talairach transform.
INFO: use src volume parameters for the talairach volume.
voxel to talairach voxel transform
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;
Calculated talairach cc position (-8.26, -12.19, 56.63)
Using the seed to calculate the cutting plane
find_cutting_plane:seed point not in structure! Searching neighborhood...
Looking for area (min, max) = (350, 1400)
area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75)
need search nearby
using seed (101, 100, 66), TAL = (-8.3, -12.2, 56.6)
talairach voxel to voxel transform
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;
talairach cc position changed to (-8.26, -12.19, 56.63)
Using voxel pons seed point, calculated talairach pons position (5.74, -1.19, 
16.63)
find_cutting_plane:seed point not in structure! Searching neighborhood...
Looking for area (min, max) = (350, 790)
area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20)
need search nearby
using seed (115, 140, 77), TAL = (5.7, -1.2, 16.6)
talairach voxel to voxel transform
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;
done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(9.74, -12.19, 56.63) SRC: 
(119.00, 100.00, 66.00)
could not find rh seed point around (119, 100, 66)

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[Freesurfer] hippocampus subfields with T2

[Alexopoulos, Dimitrios]

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We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic 
T1-mprage and a 1mm isotropic T2-space.
Is it possible or even recommended to try and generate better hippocampal 
segmentation in fressurfer 6.0 using both the T1 and T2,
or does the T2 need to be of equal or better resolution than the T1?

Jim


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Re: [Freesurfer] Vertex coordinates of pial surface: mris_convert, read_surf(), tksurfer

[Douglas N. Greve]

On 08/30/2018 02:24 PM, M. Jordan wrote:
>
> External Email - Use Caution
>
> Hello,
>
> considering the surface 'lh.pial' of the reconAll process:
>
> When I apply 'mris_convert' in order to convert to .vtk, there is a 
> shift with respect to the .pial file when viewing in freeview.
> When using the --cras_correction option for converting, the shift is 
> gone. Nevertheless, the displayed
> vertex RAS coordinates in Freeview are different. Can anyone explain 
> that? Respectively, what is '--cras_correction'actually doing?
>
> Moreover, when using the function 'read_surf()' in MATLAB to 
> read 'lh.pial' I obtain the vertex coords, but when I compare
> the vertex with index 1923 to the corresponding "Vertex RAS" in 
> tksurfer, there is a slightly mismatch.
> Can someone explain this? (I considered that MATLAB starts at index 1 
> and tksurfer at index 0!) I read, that tksurfer is actually displaying 
> the coordinates
> of the 'orig' file and not the coords of the file which is actually 
> visible? is that true?
>
> So the main questions are:
> - What are the coordinates of the 'lh.pial' file? (surface RAS / 
> tkrRAS, or something different?)
tkrRAS, see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> - Why and how do these coordinates change when converting 
> (mris_convert) or reading in MATLAB (read_surf)?
In general they should not change. but if you add --to-scanner to 
mris_convert, then it will convert the coordinates to scanner instead of 
tkrRAS
> - Is vertex with index 1000, the same after mris_convert (vtk) and 
> read_surf()?
Yes, but you need to make sure that you are taking into account that 
matlab is 1-based.
> - Why there is a mismatch between the coordinates of a certain vertex 
> in tksurfer and after read_surf
tksurfer or freeview? In fv they should be the same. In tksurfer, it may 
be giving you coordinates for the white or orig surfaces.
> - Does label2label only work with tkrRAS coordinates?
If you are using   --regmethod surface, then it does not use the 
coordinates at all (actually, it uses the spherical coords in the 
lh.sphere.reg)



> Thank you very much!!
>
>
>
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Re: [Freesurfer] MRIread error

[Douglas N. Greve]

The error message you mention ("... could not open file"). Is not in 
this recon-all.log file.

On 08/30/2018 04:23 PM, Song, Da-Yea wrote:
>  External Email - Use Caution
>
> I have attached the recon-all.log file for a different subject with the same 
> error. Hope this helps!
>
> Thanks,
> Da-yea
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
> Sent: Wednesday, August 29, 2018 4:58 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] MRIread error
>
> Can you send the recon-all.log file?
>
> On 08/29/2018 04:51 PM, Song, Da-Yea wrote:
>>   External Email - Use Caution
>>
>> There is enough disk space and it works fine with the other subjects. But 
>> for a few subjects in particular I seem to get the same error message. I 
>> checked once more and it seems that the rh.white files are being saved in 
>> the stats folder (rather than being in the "surf" folder) . The size of the 
>> files are 0KB.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>> N. Greve
>> Sent: Wednesday, August 29, 2018 4:44 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] MRIread error
>>
>> Check permissions first. Look at the size of the file. Is it much smaller 
>> than other rh.white files in other subjects? Have you run out of disk space?
>>
>> On 08/29/2018 04:37 PM, Song, Da-Yea wrote:
>>>   External Email - Use Caution
>>>
>>> Hi everyone,
>>>
>>> I'm trying to pre-process subjects through the pipeline but keep
>>> getting a handful of subjects that error out within seconds of
>>> running them. The error message I get is:
>>>
>>> MRISread(/subjects/002_1006/surf/rh.white):could not open file
>>>
>>> When I go into the subject's folder, I find the rh.white file in the
>>> stats folder. I've run about 100 subjects without an issue but for
>>> some reason there are a few subjects that will stop processing with
>>> the same error message. Any suggestions or comments would be greatly
>>> appreciated.
>>>
>>> Thanks!
>>>
>>> Dayea
>>>
>>> -
>>> -
>>> --
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>>>
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>>> D
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>>> e
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>>> Z
>>> N3Fra2zLobAGw6K3tI=
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[Freesurfer] Vertex coordinates of pial surface: mris_convert, read_surf(), tksurfer

[M. Jordan]

External Email - Use Caution

Hello,

considering the surface 'lh.pial' of the reconAll process:

When I apply 'mris_convert' in order to convert to .vtk, there is a shift with 
respect to the .pial file when viewing in freeview.
When using the --cras_correction option for converting, the shift is gone. 
Nevertheless, the displayed
vertex RAS coordinates in Freeview are different. Can anyone explain that? 
Respectively, what is '--cras_correction'actually doing?

Moreover, when using the function 'read_surf()' in MATLAB to read 'lh.pial' I 
obtain the vertex coords, but when I compare
the vertex with index 1923 to the corresponding "Vertex RAS" in tksurfer, there 
is a slightly mismatch.
Can someone explain this? (I considered that MATLAB starts at index 1 and 
tksurfer at index 0!) I read, that tksurfer is actually displaying the 
coordinates
of the 'orig' file and not the coords of the file which is actually visible? is 
that true?

So the main questions are:
- What are the coordinates of the 'lh.pial' file? (surface RAS / tkrRAS, or 
something different?)
- Why and how do these coordinates change when converting (mris_convert) or 
reading in MATLAB (read_surf)?
- Is vertex with index 1000, the same after mris_convert (vtk) and read_surf()?
- Why there is a mismatch between the coordinates of a certain vertex in 
tksurfer and after read_surf
- Does label2label only work with tkrRAS coordinates?

Thank you very much!!


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Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

[Wang, Xiaoyu]

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Thanks Martin,

Yes, I did mean to have the right hemisphere added to the left hemisphere as a 
new time point.

Can you explain on what you mean by run every subject only once?
Do you mean to run xhemi for all of the subjects and then run a paired analysis?

Xiaoyu

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[Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

[Daniel Ferreira]

External Email - Use Caution

Dear colleagues,

I was wondering if resampling voxel size is done during recon-all.

Also, I have data with voxel resolution of 1x1x1 mm at baseline and
1,2x1,2x1,2 at follow-up. I was wondering if recon-all does any computation
by default (or can be performed by any way) that minimizes these
differences in somehow.

Thank you very much

Dani

-- 

*Daniel Ferreira, PhD, Assistant Professor*

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
and Society

Karolinska Institutet (Sweden)

*Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
email: daniel.ferreira.padi...@ki.se *
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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Meena M. Makary]

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Hi;

My Linux machine has FreeSurfer 6.0 with MATLAB runtime2012bLinux (MCRv80)
which allows me to do the hippocampal subfields segmentation without
errors. Now, I'd like to use [segmentHA_T1.sh] for hippocampal and
nuclei of the amygdala segmentation which exists in the development version
of 2018 but not in vr 6.0. I copied this bash file and other related files
from the development version to my vr 6.0 /freesurfer/bin directory but I
stuck with errors related to the MATLAB runtime version (it needs MCRv84).
I downloaded runtime2014bLinux (MCRv84), but still same errors. Any
recommendation to overcome this problem?.
Will it be okay if I just replaced my vr6.0 /freesurfer/bin folder by the
one from the recent development version? - given that I analyzed my data
using recon-all by vr6.0.

Thanks;
--Meena

-- 

*Meena M. Makary, Ph.D.*
Assistant Professor | Cairo University 
Postdoctoral Fellow | Yale University School of Medicine

Postdoctoral Associate |  The John B. Pierce Laboratory

Treasurer | OHBM Student and Postdoc SIG


290 Congress Avenue, New Haven, CT 06519
+1 (475) 731-5592 <+1%20475-731-5592>
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Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Shatil, Anwar Shahadat]

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Hello Martin:

I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42 (that came 
with it by default).

If I omit --out-pc1 but keep --do-pc1 still do not get any output as a .dat or 
.stats file. I only get .mgh file in surf folder.

I need percentage change values of tp2 from tp1 for each subject in a tabular 
form.

Best,

Anwar

On 2018-08-30, 3:22 AM, "Martin Reuter"  wrote:

Hi Anwar,

what FS version are you using?

Also what happens if you omit the --out-pc1 but keep the --do-pc1 ?
Also no output with that ending? It should write it to the default
location.

Best, Martin





On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat wrote:
> External Email - Use Caution
> Dear Doug:
>
> I am trying to get a table containing pc1 values for each subject in
> a longitudinal study and failed to extract this. I use the code
> below:
>
> long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> --time years --qcache fsaverage --sd
> /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat
>
> It says
> long_mris_slopes: error: no such option: --out-pc1
>
>
> However in the --help file it says:
>
> Within-Subject Output:
> Pass these to overwrite the default names:
>
> --out-avg=OUT_AVG   filename to store temporal average in
> /stats/ (default:
> long..-avg.dat)
> --out-rate=OUT_RATE
> filename to store rate in
> /stats/
> (default: long..-rate.dat)
> --out-pc1fit=OUT_PC1FIT
> filename to store pct. change (to tp1fit) in
> /stats/ (default:
> long..-pc1fit.dat)
> --out-pc1=OUT_PC1   filename to store pct. change (to tp1) in
> /stats/ (default:
> long..-pc1.dat)
> --out-spc=OUT_SPC   filename to store sym. pct. change in
> /stats/ (default:
> long..-spc.dat)
> --out-resid=OUT_RESID
> filename to store residual in
> /stats/ (default:
> long..-resid.dat),
> requires
> --resid 
> --out-stack=OUT_STACK
> filename to store stacked measure file
> /stats/ (default:
> long..-stack.dat)
>
>   Stacked Tables:
> To output tables with results from all subjects
>
> --stack-avg=STACK_AVG
> full filename to stack temporal average
> tables
> (default no stacking)
> --stack-rate=STACK_RATE
> full filename to stack rate tables (default
> no
> stacking)
> --stack-pc1fit=STACK_PC1FIT
> full filename to stack pct. change to tp1fit
> tables
> (default no stacking)
> --stack-pc1=STACK_PC1
> full filename to stack pct. change to tp1
> tables
> (default no stacking)
> --stack-spc=STACK_SPC
> full filename to stack sym. pct. tables
> (default no
> stacking)
> --stack-resid=STACK_RESID
> full filename to stack residual tables
> (default no
> stacking)
>
>
> Am I writing the code wrong?? I never got any long..-
> pc1.dat file in /stats/ folder except bunch of mgh files
> in /surf/ folder.
>
> Thanks,
>
> Anwar
> --
>
> Anwar S. Shatil
>
> Research Assistant
> Department of Medical Imaging
> Sunnybrook Health Sciences Centre
> Room AB204, 2075 Bayview Avenue
> Toronto, ON M4N 3M5
> Tel: 416.480.6100 ext. 89617
> Email: anwar.sha...@sunnybrook.ca
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[Freesurfer] Fwd: Biomedical Research Engineer Position

[Florence M]

External Email - Use Caution

Title : *Biomedical **Research Engineer*
No. of Position(s): One (1) position
Location  : Paris, France
Starting date   : November 2018


*JOB DESCRIPTION*

The successful applicant will work in the Group of Clinical Research on
Alzheimer Precision Medicine (GRC-APM) at the site of Pitié-Salpêtrière
Hospital of Sorbonne University under the supervision of Prof. Harald
Hampel, holder of AXA Research Fund & Sorbonne University Chair « sur le
dépistage de la maladie d’Alzheimer».

The GRC-APM has as main objective the advancements in detecting, treating,
and preventing Alzheimer’s disease (AD) by the implementation of a
Precision Medicine (PM) strategy. The successful applicant will be tasked
with coding in efficient ways analytical methods and build internal
capabilities and gears for these methods. He/she would also be responsible
for setting up and running statistical and neuroimaging analysis pipelines
for scientific studies. It would be expected for the Biomedical Research
Engineer to regularly monitor and assess data quality for on-going projects
and provide feedback to collaborators.



*Duties include:*

   - To develop MRI pipelines and data analyses in particular DTI data and
   their integration with structural MRI and functional MRI
   - To support researchers in the team during the scientific writing
   process
   - To manage the internal database, which may include the development of
   new user interfaces.

*Desired qualifications:*

   - Experienced in processing structural MRI and DTI neuroimaging data
   - Demonstrated high level capacity for scripting with different
   languages, such as Python, R, MATLAB
   - Familiarity with system administration, project and neuroimaging data
   management
   - Familiarity with neurological concepts and/or experience with
   Alzheimer’s disease is desirable
   - Ability to integrate multimodal data, including neuroimaging data,
   biological markers and genetic data will be appreciated.


*Education & experience *

Master's degree Biomedical Research Engineer or related field. Two years of
relevant experience is

 highly desirable though not necessary

*Knowledge, skills and abilities:*

   - Strong analytical and organizational skills.
   - Ability to learn and utilize relational databases, data integration,
   and statistics.
   - Strong written and oral English communication skills.
   - Ability to understand scientific literature, experimental procedures
   and their limitations, and current needs of the research community, as
   applied in clinical neuroscience and neuroimaging research.

Position length: The position is supported for 4 years. However, candidates
will be appointed for 1 year, with an extension possible based on progress



Salary: 2,183 € gross / month



Please send a brief letter of motivation and your detailed CV as one pdf
(<2MB) to patrizia.chi...@icm-institute.org
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[Freesurfer] Fwd: Postdoctoral Position on Imaging Genetics

[Florence M]

External Email - Use Caution

Title : *Postdoctoral Position on Imaging
Genetics*
No. of Position(s): One (1) position
Location  : Paris, France
Starting date   : November 2018

*JOB DESCRIPTION*

The successful applicant will work in the Clinical Research Group on
Alzheimer Precision Medicine (GRC-APM) at the site of Pitié-Salpêtrière
Hospital of Sorbonne University under the supervision of Prof. Harald
Hampel, holder of AXA Research Fund & Sorbonne University Chair « *sur le
dépistage de la maladie d’Alzheimer*».

The GRC-APM has as main objective the advancements in detecting, treating,
and preventing Alzheimer’s disease (AD) by the implementation of a
Precision Medicine (PM) strategy. The successful applicant will collaborate in
the area of imaging genetics involving the development of algorithms for
the identification of novel multi-modal (imaging and genetic) feature
combinations and probabilistic models that explain these imaging-genetic
interactions and facilitate diagnoses and prognoses in cognitive intact
older adults at risk for AD and AD dementia patients. The candidate will
benefit from the collaboration with our multidisciplinary team members and
from our on-going collaborations with European and US research centres.



*JOB RESPONSIBILITIES*



·   To conduct analyses of neuroimaging and genetics data on large
datasets

·   To develop statistical models and/or use softwares that
incorporates information across different modalities of data such as
imaging (3D-T1; rs-fMRI; DTI; amyloid-Pet and FDG-PET, genetic, gene
expression, biofluids)

·   To write scientific publications

·   To collaborate with other Team research scientists

·   To present findings at international conferences


* EDUCATION*

PhD in bio-/Statistics, Computer Science, Machine Learning, Electrical
Engineering or related fields, with research experience in statistical
machine learning using complex multivariate data.




*KNOWLEDGE – SKILLS – ABILITIES*

Experience on probabilistic graphical models, and/or dimensionality reduction,
and and/or sparse learning is highly desirable. Researchers with image
processing pipelines and gene expression analysis are particularly
encouraged to apply. Strong programming skills (working knowledge of Linux,
C/C++, Python, Matlab) is desirable

*REQUIREMENTS*

The candidate for this position is expected to have: strong background in
machine learning, advanced statistical modeling and data analysis, possess
excellent writing and communication skills. Experience in biostatistics and
particularly analyzing genetic and imaging data.





Position length: The position is supported for 4 years. However, candidates
will be appointed for 1 one year, with an extension possible based on
progress


Salary: The salary compensation is very competitive: 3700,00 € gross /
month


Please send a brief letter of motivation and your detailed CV as one pdf
(<2MB) to patrizia.chi...@icm-institute.org
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Fwd: Biostatistician Position

[Florence M]

External Email - Use Caution

Title : Biostatistician
No. of Position(s): One (1) position
Location  : Paris, France
Starting date   : as soon as possible

*JOB DESCRIPTION*

The successful applicant will work at the Pitié-Salpêtrière
University-hospital site under the supervision of Prof. Harald Hampel,
holder of AXA Research Fund & Sorbonne University Chair « sur le dépistage
de la maladie d’Alzheimer».

The AXA Research Fund & Sorbonne University Chair conceptualized that
substantial advancements in detecting, treating, and preventing Alzheimer’s
disease (AD) will evolve from the generation and systematic implementation
of a Precision Medicine (PM) strategy. The successful applicant will
collaborate on several projects and cohorts around AD, as the sole
statistician of a six-member research group but will also interact with
other statisticians at the Pitié-Salpêtrière University-hospital.


*JOB RESPONSIBILITIES*

§  Analyzing data and assisting in the interpretation of the results

§  Performing sample size and power calculations

§  Making recommendations to the Team members for the appropriate design of
statistical analyses

§  Performing analyses of “big and deep data”, including omic(s) data, and
genetic epidemiology data

§  Writing program codes to analyze data via statistical analysis software

§  Responsible for suitability, accuracy, and timeliness of statistical
inputs into reports and projects

§  Interacting with other Team research scientists, external statisticians,
and data managers in the analyses of the results, interpretation of
biostatistical findings, and collection of the information for formulating
advanced statistical programs



* EDUCATION*

§  Master’s degree or PhD in Statistics, Biostatistics or related areas
(e.g., Bioinformatics).


*KNOWLEDGE – SKILLS – ABILITIES*

Expertise in statistical software such as R, Python, Matlab and working
knowledge of data management softwares such as Microsoft Excel and
Microsoft Access
Expertise in basic and advanced statistical analyses (such as Bayesian
statistics)
 High proficient level of English (both in oral communications and in
writing) is mandatory


*REQUIREMENTS*

§  A minimum of 2 years (for Master’s degree education level) of
demonstrated experience in statistical analyses and in summarizing findings

Position length: The position is supported for 3 years. However, candidates
will be appointed for 1 year, with an extension possible based on progress


Salary: between 2,183 € gross / month and 2,443 € gross / month



Please send a brief letter of motivation and your detailed CV as one pdf
(<2MB) to *patrizia.chi...@icm-institute.org
*
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] freesurfer development version for mac incomplete

[Hoopes, Andrew]

The centos dev version can be downloaded from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos7_x86_64-dev.tar.gz.
 What link can you not access?
Best,
Andrew


From:  on behalf of "Scheffler, F, Mev 
[fre...@sun.ac.za]" 
Reply-To: FS Help 
Date: Thursday, August 30, 2018 at 2:23 AM
To: FS Help 
Subject: Re: [Freesurfer] freesurfer development version for mac incomplete


External Email - Use Caution
Dear FreeSurfer developers

I’m struggling to download the linux development version, could you please send 
me the link?

This mac version you sent to Ani downloaded fine, but I just can’t access the 
linux version link through the website and we’ve been trying for weeks now 
already.

Thanks!

Kind regards,




FREDA SCHEFFLER

Research Assistant / PhD Candidate


[email.jpg]


MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika

Tel:  +27 21 938 9771
Email | E-pos:  fre...@sun.ac.za




From:  on behalf of "Hoopes, Andrew" 

Reply-To: Freesurfer support list 
Date: Monday, 27 August 2018 at 17:01
To: Freesurfer support list 
Cc: "aniqa...@gmail.com" 
Subject: Re: [Freesurfer] freesurfer development version for mac incomplete

Hi Ani, are you using 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz
 and are you sure the downloaded fully completed?

Best,
Andrew

From:  on behalf of Anik Dar 

Reply-To: FS Help 
Date: Monday, August 27, 2018 at 8:46 AM
To: FS Help 
Subject: [Freesurfer] freesurfer development version for mac incomplete


External Email - Use Caution
Hi

When I try to download the development version of freesurfer for mac, the file 
size is only 138 MB and doesnt unzip once downloaded.

Is there another link where the complete development version for mac can be 
found ?

Thanks

Ani
[Image removed by 
sender.]

The integrity and confidentiality of this email are governed by these terms. 
Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende 
bepalings bereël. Vrywaringsklousule
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Martin Reuter]

Hi Anwar, 

what FS version are you using?

Also what happens if you omit the --out-pc1 but keep the --do-pc1 ?
Also no output with that ending? It should write it to the default
location. 

Best, Martin





On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat wrote:
> External Email - Use Caution
> Dear Doug:
> 
> I am trying to get a table containing pc1 values for each subject in
> a longitudinal study and failed to extract this. I use the code
> below:
> 
> long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> --time years --qcache fsaverage --sd
> /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat
> 
> It says 
> long_mris_slopes: error: no such option: --out-pc1
> 
> 
> However in the --help file it says:
> 
> Within-Subject Output:
>     Pass these to overwrite the default names:
> 
>     --out-avg=OUT_AVG   filename to store temporal average in
>                         /stats/ (default:
>                         long..-avg.dat)
>     --out-rate=OUT_RATE
>                         filename to store rate in
> /stats/
>                         (default: long..-rate.dat)
>     --out-pc1fit=OUT_PC1FIT
>                         filename to store pct. change (to tp1fit) in
>                         /stats/ (default:
>                         long..-pc1fit.dat)
>     --out-pc1=OUT_PC1   filename to store pct. change (to tp1) in
>                         /stats/ (default:
>                         long..-pc1.dat)
>     --out-spc=OUT_SPC   filename to store sym. pct. change in
>                         /stats/ (default:
>                         long..-spc.dat)
>     --out-resid=OUT_RESID
>                         filename to store residual in
>                         /stats/ (default:
>                         long..-resid.dat),
> requires
>                         --resid 
>     --out-stack=OUT_STACK
>                         filename to store stacked measure file
>                         /stats/ (default:
>                         long..-stack.dat)
> 
>   Stacked Tables:
>     To output tables with results from all subjects
> 
>     --stack-avg=STACK_AVG
>                         full filename to stack temporal average
> tables
>                         (default no stacking)
>     --stack-rate=STACK_RATE
>                         full filename to stack rate tables (default
> no
>                         stacking)
>     --stack-pc1fit=STACK_PC1FIT
>                         full filename to stack pct. change to tp1fit
> tables
>                         (default no stacking)
>     --stack-pc1=STACK_PC1
>                         full filename to stack pct. change to tp1
> tables
>                         (default no stacking)
>     --stack-spc=STACK_SPC
>                         full filename to stack sym. pct. tables
> (default no
>                         stacking)
>     --stack-resid=STACK_RESID
>                         full filename to stack residual tables
> (default no
>                         stacking)
> 
> 
> Am I writing the code wrong?? I never got any long..-
> pc1.dat file in /stats/ folder except bunch of mgh files
> in /surf/ folder.
> 
> Thanks,
> 
> Anwar
> --
> 
> Anwar S. Shatil
> 
> Research Assistant
> Department of Medical Imaging
> Sunnybrook Health Sciences Centre
> Room AB204, 2075 Bayview Avenue
> Toronto, ON M4N 3M5
> Tel: 416.480.6100 ext. 89617
> Email: anwar.sha...@sunnybrook.ca
> This e-mail is intended only for the named recipient(s) and may
> contain confidential, personal and/or health information (information
> which may be subject to legal restrictions on use, retention and/or
> disclosure).  No waiver of confidence is intended by virtue of
> communication via the internet.  Any review or distribution by anyone
> other than the person(s) for whom it was originally intended is
> strictly prohibited.  If you have received this e-mail in error,
> please contact the sender and destroy all copies.
>  
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Re: [Freesurfer] error in longitudinal stream command

[Martin Reuter]

Hi Valeria, 

that is a local install (a frozen version of 5.3 or some modified
version from 2013). 

Can you source the system wide install of 5.3 and test that.
source /space/freesurfer/nmr-stable53-env

If that fails, try 6.0
source /space/freesurfer/nmr-stable60-env

Also make sure all directories exist, are filled with data and are
readable. You can also check the base-tps file in the base and see if
all time points are listed there correctly. 

As a last resort, you can try to re-run the base from scratch and then
the long again from scratch. If all that fails, it could be a bug in
recon-all (maybe it get's confused with all the _ in the name, but that
is unlikely. I also remember we had difficulties with really long names
in 5.3 but then it should work with 6.0. 

Best, Martin


On Wed, 2018-08-29 at 17:41 +, Barletta, Valeria wrote:
> Hi Martin, thanks for your reply.
> I tried to re-type the command in the shell but I still have the
> error.
> I don't know what you mean with system install, but we are using the
> version 5.3 and this is the path, if it can help:
> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/freesurfer-
> stable5_3_0-05152013
> 
> Thank you!
> Valeria
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.
> mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.
> edu]
> Sent: Wednesday, August 29, 2018 12:14 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] error in longitudinal stream command
> 
> Hi Valeria,
> 
> what version of FS are you using (also is it a local install or the
> system install)?
> 
> Also try to re-type the command in the shell (don't run it from a
> script) could be that there are invisible characters , like tab etc
> from copy paste that mess things up.
> 
> Best, Martin
> 
> 
> On Wed, 2018-08-29 at 13:51 +, Barletta, Valeria wrote:
> > Dear Freesurfers,
> > I am trying to re-launch a longitudinal time point after edits by
> > using the command:
> > 
> > recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base
> > MS069_base -all
> > 
> > But I am obtaining this type of error:
> > 
> > Unmatched ".
> > 
> > I also tried to launch it on Launchpad but I have an error all the
> > same and the process immediately aborts.
> > Do you know what could be the reason?
> > Thank you,
> > Valeria
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 
> 
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] freesurfer development version for mac incomplete

[Scheffler, F, Mev [fre...@sun.ac.za]]

External Email - Use Caution

Dear FreeSurfer developers

I’m struggling to download the linux development version, could you please send 
me the link?

This mac version you sent to Ani downloaded fine, but I just can’t access the 
linux version link through the website and we’ve been trying for weeks now 
already.

Thanks!

Kind regards,




FREDA SCHEFFLER

Research Assistant / PhD Candidate


[email.jpg]


MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika

Tel:  +27 21 938 9771
Email | E-pos:  fre...@sun.ac.za




From:  on behalf of "Hoopes, Andrew" 

Reply-To: Freesurfer support list 
Date: Monday, 27 August 2018 at 17:01
To: Freesurfer support list 
Cc: "aniqa...@gmail.com" 
Subject: Re: [Freesurfer] freesurfer development version for mac incomplete

Hi Ani, are you using 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz
 and are you sure the downloaded fully completed?

Best,
Andrew

From:  on behalf of Anik Dar 

Reply-To: FS Help 
Date: Monday, August 27, 2018 at 8:46 AM
To: FS Help 
Subject: [Freesurfer] freesurfer development version for mac incomplete


External Email - Use Caution
Hi

When I try to download the development version of freesurfer for mac, the file 
size is only 138 MB and doesnt unzip once downloaded.

Is there another link where the complete development version for mac can be 
found ?

Thanks

Ani
[http://cdn.sun.ac.za/100/ProductionFooter.jpg]

The integrity and confidentiality of this email are governed by these terms. 
Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende 
bepalings bereël. Vrywaringsklousule
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.