Re: [Freesurfer] Interpreting Covariate Paired Analysis Results

[Douglas N. Greve]

Can you say more about your approach? Are you subtracting the two time 
points explicitly and computing a paired t? Or are you using the 
repeated measures anova approach. Send the FSGD file


On 11/30/2021 11:04 AM, PDMD SRALab wrote:


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We are using a paired analysis approach to study cortical thickness in 
a dataset with 2 timepoints (called pre-protocol and post-protocol). 
Regarding the mean cluster summary (contrast: [1 0]), we understand 
positive values to mean pre > post (thinning) and negative values to 
mean post > pre (thickening). The covariate results are more difficult 
to interpret. For instance, we’re interested in looking at the effects 
of age (contrast: [0 1]) on the cortical thickness results. In the age 
cluster summary, is it fair to interpret positive results as positive 
correlation (older subjects show more thickening) and negative results 
as inverse correlation (older subjects show more thinning) or is the 
interpretation more complex than this? We’re getting mainly negative 
cluster results for age so this interpretation may make sense, but 
we’d like more clarity. Thank you for your help.



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Re: [Freesurfer] White matter

[Douglas N. Greve]

You can merge them yourself or you could run mri_annotation2label with 
one of the --lobes options to generate a new annotation of lobes, run 
use that to generate a new wmparc.mgz file (look in the recon-all.log 
file to get the command, specify your new annotation and change the 
output file name).


On 12/7/2021 9:23 AM, Paul, Rahul wrote:

Hi FreeSurfer experts,

I know that FreeSurfer genrates WM information (area/volume) for 
smaller cortical regions (e.g, superiortemporal, supramarginal) along 
with the GM information.
But, I was wondering is there a way to generate larger WM structures 
(e.g., temporal lobe or parietal lobe) using freesurfer?


Thank you,

Rahul

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Re: [Freesurfer] error in mri_sclimbic_seg

[Douglas N. Greve]

Hard to say what is going wrong from that. Can you try removing the 
trailing "/" from the subject name? Also, do you need --conform? Often 
the recon-all output is already conformed, so --conformed is not usually 
needed. It would be interesting to know if this is making it fail.


On 12/6/2021 5:40 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:


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I receive this error when I try to run mri_sclimbic_seg in dev 2021 12 06

How can I fix this?

mri_sclimbic_seg --s 10105_S1200QUM/ --conform
/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg --s 
10105_S1200QUM/ --conform

Excluding seg [853]
Using CPU
Using 1 thread(s)
Loaded lookup table /usr/local/freesurfer/dev7/models/sclimbic.ctab
Loaded population stats 
/usr/local/freesurfer/dev7/models/sclimbic.volstats.csv

Segmentation fault

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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Re: [Freesurfer] Definition of Premotor Area

[Douglas N. Greve]

Is the problem that there is an overlap? The exvivo labels and aparc 
labels are not going to be mutually exclusive.


On 12/6/2021 5:34 PM, Tsolaki, Evangelia C. wrote:


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Hello Freesurfer Team,

I am interested in using premotor, precentral gyrus and postcentral 
gyrus in my analysis.


For the definition of the precentral gyrus and postcentral gyrus I use 
the following lines:


fslmaths aparc+aseg.nii.gz -thr 1024 -uthr 1024 PreCG_L.nii.gz

fslmaths aparc+aseg.nii.gz -thr 2024 -uthr 2024 PreCG_R.nii.gz

fslmaths aparc+aseg.nii.gz -thr 1022 -uthr 1022 PostCG_L.nii.gz

fslmaths aparc+aseg.nii.gz -thr 2022 -uthr 2022 PostCG_R.nii.gz

To define the premotor area I use the labels rh.BA6_exvivo.label  and 
lh.BA6_exvivo.label according to the script below:


bbregister --s SubID_FreeSurfer --mov nodif.nii.gz --reg lowb2orig.dat 
--dti --init-fsl


mri_label2vol --label SubID_FreeSurfer /label/rh.BA6_exvivo.label  
--reg lowb2orig.dat  --fillthresh .3 --hemi rh --subject 
SubID_FreeSurfer --o BA6_R.nii.gz --temp nodif.nii.gz --proj frac 0 1 .1


When I check the location of the resulted BA6 and precentral gyrus 
masks, there is an overlap. Could you please advise if there is any 
other way to define premotor area?


Thank you in advance,

Evie




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Re: [Freesurfer] question about surface registration to an average surface

[Douglas N. Greve]

How did you create the new MNI chimp average surface?

On 12/5/2021 11:08 AM, Trisanna Sprung-Much wrote:


External Email - Use Caution

Hi Bruce

So I have 77 chimp scans reconstructed in FS (NOT registered to MNI 
space, but rather a chimp volume template, to avoid scaling). After a 
lot of trial and error, we got some really nice surfaces.


I tried to use make_average_surface this summer and I was running into 
one problem after the next and unfortunately no one answered my 
questions. So, we have a new MNI chimp average surface and I would 
like to know if I can somehow implement this average surface into FS 
to perform surface registration of my individual labels to the average 
surface.


Thanks!
Trisanna

--



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


*Sent:* Sunday, December 5, 2021 12:03 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] question about surface registration to an 
average surface


I’m not really sure what you are trying to do, but I guess you will 
want to make your own average. I think there is a new script for this, 
so someone else will have to comment


Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Trisanna 
Sprung-Much

*Sent:* Saturday, December 4, 2021 10:00 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] question about surface registration to an 
average surface


*External Email - Use Caution *

Thanks Bruce  Yes I am working with chimp data.

Any other things I could try?

Trisanna

Sent from my Galaxy

 Original message 

From: "Fischl, Bruce" 

Date: 2021-12-04 11:12 a.m. (GMT-05:00)

To: Freesurfer support list 

Subject: Re: [Freesurfer] question about surface registration to an 
average surface


Oh, then no, that won’t work

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Trisanna 
Sprung-Much

*Sent:* Saturday, December 4, 2021 10:48 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] question about surface registration to an 
average surface


*External Email - Use Caution *

Hi Bruce, I will try mris_sphere! But since this is a chimp average, 
when you say then register it to your atlas- is this something I 
should do?


Trisanna

Sent from my Bell Samsung device over Canada's largest network.

 Original message 

From: "Fischl, Bruce" 

Date: 2021-12-04 10:27 a.m. (GMT-05:00)

To: Freesurfer support list 

Subject: Re: [Freesurfer] question about surface registration to an 
average surface


Hi Trisanna

Can you run mris_sphere on it to create a spherical surface? You could 
then register that to our atlas using mris_register. You will need to 
create a bunch of files that we expect though like ?h.curv, ?h.sulc, 
etc…  You might also need to specify a volume, but I expect any 
conformed one will be ok


Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Trisanna 
Sprung-Much

*Sent:* Friday, December 3, 2021 6:42 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] question about surface registration to an 
average surface


*External Email - Use Caution *

Hi there

I have a bunch of labels on individual subjects and would like to 
register them to an average surface that we have created here at the 
MNI. So, this average has not gone through recon-all and there are no 
freesurfer recon-all files associated with it. There is no volume 
associated with it to run in recon-all.


According to the instructions for mri_surf2surf I need the sphere.reg 
file, which is generated during recon-all. I wonder if there is a way 
to undergo surface registration in my situation? I found the following 
documentation, but this seems to be for creating a new average. I have 
the average already.


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 



SurfaceRegAndTemplates - Free Surfer Wiki 



The output from registration is yet another 

Re: [Freesurfer] Questions about GLM

[Douglas N. Greve]

If you run it with --eres-save, it will save the residuals in eres.mgh

On 12/4/2021 11:17 AM, Laura Willers de Souza wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I would like to assess whether my regression model meets the GLM 
assumptions, especially if there is no multicollinearity.


Is it possible to perform this diagnosis in freesurfer?

If not, is there a way to extract the model residues to test in 
another program?


Or, is there any way to perform a regression with correlated variables 
in freesurfer?



Thanks in advance!

*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


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Re: [Freesurfer] mri_label2label: one-to-one for subjectNo --> ico

[Douglas N. Greve]

Don, can you send your command line? If you are using surface-based 
registration, then the origin should not matter. You are right that 
there is not a one-to-one correspondence. The way it works  is that it 
starts on the target surface, goes through all the vertices and finds 
the closest vertex in the source and maps the value. At this point, each 
target only has one source, but each source may have multiple targets. 
By default, it then goes through another loop where it finds all the 
source vertices that have not been mapped, finds the closest target 
vertex, and  maps the source to that target (eventually taking the mean 
or sum of all the sources that map to a given target). If it is the 2nd 
stage that is giving you problems, then you can turn it off in 
mris_apply_reg with --nnf (stands for "nearest-neighbor-forward", vs the 
default nnfr where r=reverse).



On 12/3/2021 8:41 AM, Krieger, Donald N. wrote:


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Dear Bruce, Doug, and everyone,

 1. I am projecting labels from a subject’s labels onto the
icosahedron and note that the mapping is not one-to-one. Because
of this, I cannot tell which subject vertex maps to which
icosahedron vertex which I need to able to do. What am I missing here?
 2. Just double-checking something simple – The center of the
icosahedron is as the origin, i.e. 0,0,0, yes?

Thanks – Don


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Re: [Freesurfer] Help

[Douglas N. Greve]

The data look pretty noisy in those images. My guess is that the WM is 
not getting segmented properly in that temporal area or there is an 
incorrectly fixed topology error. Try looking at the wm.mgz (or the 
filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz to 
see where the defects are.


On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:


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Sure. See attached.

//Nilab

*From:* Douglas N. Greve 
*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah ; 
freesurfer@nmr.mgh.harvard.edu 

*Subject:* Re: [Freesurfer] Help
Can you send them in plain, unzipped format?

On 11/29/2021 4:07 AM, Nilab Nasrullah wrote:


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I am attaching a few screenshots of the segmented brain as zip-files. 
Hopefully, you can see the results. If not, let me know so I can send 
it to you in a different format.


Thanks,
Nilab

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
 
 on behalf of Douglas 
N. Greve  

*Sent:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] Help
Can you send some pictures?

On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:


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Hi,

I am editing subjects for a research project. After reconstruction, 
some parts of the brain are not included in the segmentation. Often, 
some parts of the temporal lobe and the cortex of the occipital lobe 
are not included. In some cases, the cortex of the frontal lobe is 
also affected.


I have tried using controls points, but the results don't change. I 
have also reconstructed them again, running autorecon1 and 
autorecon2&3 separately. I have lowered the watershed parameters, 
used the gcut command and edited manually after autorecon1 but in 
the end, the results don't vary significantly compared to running 
recon-all -all.


What can I do to include the missing parts?

Thanks,
Nilab



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Re: [Freesurfer] mri_gcut gives "error: Could not set locale"

[Douglas N. Greve]

are you just running gcut or all of recon-all? If all of recon-all, 
please send the recon-all.log file


On 12/2/2021 2:43 PM, Vishal Mohanty wrote:


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Hi

This is Vishal Mohanty, a Research Assistant at the CNS Lab 
 
at Stanford which is headed by Prof. Kilian Pohl 
. 
We are running Freesurfer commands for processing of our MRI data on 
Sherlock 
 
which is the HPC cluster at Stanford. We are seeing some errors in 
running *mri_gcut* of the type:


CREATE 
LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/gcut_t1b_brain.nii.gz




error: No such file or directory

error: Could not set locale^@


I'm attaching the full log file. Could you please help me understand 
what's the issue and how to fix it. Do let me know what other 
information would be needed from my end.


Thanks and Regards

Vishal Mohanty
MS CS Candidate (2023)
Stanford University

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Re: [Freesurfer] Qdec error

[Douglas N. Greve]

We are not supporting qdec anymore. Try using the "command line stream", 
ie, mris_preproc, FSGD, etc


On 12/1/2021 6:47 PM, Arian Klows wrote:


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 Dear FS experts,

I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I 
run qdec, I get the following error:


Tk_Init error: invalid command name "tcl_findLibrary"
Error initializing Tcl.

Could anyone please tell me what this means?

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Re: [Freesurfer] FSGD file

[Douglas N. Greve]

There is no way to model a missing cell in the FSGD. You'd have to 
figure out a value (eg, using imputation) or exclude those subjects


On 11/30/2021 2:59 PM, Laura Willers de Souza wrote:


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Hello FreeSurfer Developers,

I would like to know what I put in the FSGD file for patients who 
don't have data for a variable.


In my case, I want to analyze CU (cognitively unimpaired) patients 
versus CI (cognitively impaired) patients, controlling for CSF and 
plasma cortisol values. And some patients have only the CSF value and 
others only the plasma value.


Would the analysis be correct if I put the mean of the non-missing 
values of this variable in those cells that don't have data?


Would you be so kind to help me with that?

Thanks in advance!

Laura.

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Re: [Freesurfer] REtrieve perimeter from generated surfaces

[Douglas N. Greve]

sorry, I don't know what you mean by perimeter

On 11/29/2021 8:09 PM, Fernanda Hansen P. de Moraes wrote:


External Email - Use Caution

Dear FreeSurfer experts,

Is there a way to estimate the perimeter from a surface (e.g. ?h.pial) 
for each slice in an automated manner at any orientation?


Thank you very much,
Fernanda Hansen P. de Moraes

fernandahmor...@gmail.com
Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino e 
metaBIO (IF-UFRJ)


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Re: [Freesurfer] Information on anova 2x2 longitudinal design

[Douglas N. Greve]

you need to run it as a DOSS, ie, --fsgd Repeted_measure.fsgd  doss

On 11/29/2021 6:50 PM, std...@virgilio.it wrote:


External Email - Use Caution

Hi list,

I have two groups undergoing two different treatments: one's placebo 
(n=12), one's drug (n=12). Two timepoints, at baseline (T1, no 
treatment) and at treatment (T2). 2x2 ANOVA, repeted measures has been 
applied by following the guidlines and mailing list.


Please chech the design matrix, the command line produces an error.

GroupDescriptorFile 1
Title 2x2_repeted_measures
Class Subject1
Class Subject2
Class Subject3
Class Subject4
Class Subject5
Class Subject6
Class Subject7
Class Subject8
Class Subject9
Class Subject10
Class Subject11
Class Subject12
Class Subject13
Class Subject14
Class Subject15
Class Subject16
Class Subject17
Class Subject18
Class Subject19
Class Subject20
Class Subject21
Class Subject22
Class Subject23
Class Subject24
Variables tp1-vs-tp2.drug tp1-vs-tp2.plb
Input CODE01_tp1 Subject1 1 0
Input CODE02_tp1 Subject2 1 0
Input CODE03_tp1 Subject3 1 0
Input CODE05_tp1 Subject4 1 0
Input CODE06_tp1 Subject5 0 1
Input CODE07_tp1 Subject6 0 1
Input CODE09_tp1 Subject7 0 1
Input CODE10_tp1 Subject8 1 0
Input CODE11_tp1 Subject9 1 0
Input CODE12_tp1 Subject10 0 1
Input CODE13_tp1 Subject11 0 1
Input CODE14_tp1 Subject12 1 0
Input CODE15_tp1 Subject13 1 0
Input CODE16_tp1 Subject14 1 0
Input CODE17_tp1 Subject15 0 1
Input CODE18_tp1 Subject16 1 0
Input CODE19_tp1 Subject17 0 1
Input CODE20_tp1 Subject18 0 1
Input CODE21_tp1 Subject19 0 1
Input CODE22_tp1 Subject20 1 0
Input CODE23_tp1 Subject21 0 1
Input CODE24_tp1 Subject22 0 1
Input CODE25_tp1 Subject23 1 0
Input CODE26_tp1 Subject24 0 1
Input CODE01_tp2 Subject1 -1 0
Input CODE02_tp2 Subject2 -1 0
Input CODE03_tp2 Subject3 -1 0
Input CODE05_tp2 Subject4 -1 0
Input CODE06_tp2 Subject5 0 -1
Input CODE07_tp2 Subject6 0 -1
Input CODE09_tp2 Subject7 0 -1
Input CODE10_tp2 Subject8 -1 0
Input CODE11_tp2 Subject9 -1 0
Input CODE12_tp2 Subject10 0 -1
Input CODE13_tp2 Subject11 0 -1
Input CODE14_tp2 Subject12 -1 0
Input CODE15_tp2 Subject13 -1 0
Input CODE16_tp2 Subject14 -1 0
Input CODE17_tp2 Subject15 0 -1
Input CODE18_tp2 Subject16 -1 0
Input CODE19_tp2 Subject17 0 -1
Input CODE20_tp2 Subject18 0 -1
Input CODE21_tp2 Subject19 0 -1
Input CODE22_tp2 Subject20 -1 0
Input CODE23_tp2 Subject21 0 -1
Input CODE24_tp2 Subject22 0 -1
Input CODE25_tp2 Subject23 -1 0
Input CODE26_tp2 Subject24 0 -1

a) groupxtime.mtx 0 0 1 -1
b) tp1-vs-tp2.Mod.mtx 0 0 1 0
c) tp1-vs-tp2.Plb.mtx 0 0 0 -1

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh 
--glmdir repeted_measures.wls --nii.gz --fsgd Repeted_measure.fsgd --C 
Tp1-vs-Tp2.Mod.mtx --C Tp1-vs-Tp2.Plb.mtx --C groupxtime.mtx


ERROR: dimension mismatch between X and contrast Tp1-vs-Tp2.Mod.mtx 
  X has 72 cols, C has 4 cols



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Re: [Freesurfer] Errors with mkanalysis-sess: missing file fmcpr.brainmask.fsaverage.lh

[Douglas N. Greve]

Try removing the mask and funcstem flags

On 11/29/2021 12:49 PM, Hiersche, Kelly J. wrote:


External Email - Use Caution

Hello,

I was adapting existing code in my lab that was used for doing a 
volume-based analysis, so I tried to keep the inputs the same.


Do you think removing the mask flag would be helpful?

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, November 29, 2021 12:28 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Errors with mkanalysis-sess: missing file 
fmcpr.brainmask.fsaverage.lh
In your mkanalysis command, why are you specifying the mask and the 
funcstem? These are tricky options to get right ...


On 11/29/2021 9:50 AM, Hiersche, Kelly J. wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

First, I am new to using Freesurfer, so I apologize if any 
information is unclear.


I am attempting to use the following tutorial *MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel 
 to 
do a surface based GLM in an individual subject (using my own data, 
not the tutorial data), but I am getting the following error:


Error using MRIread (line 76)
ERROR: cannot determine format of
/*subnum/bold/runnum/masks*/fmcpr.brainmask.fsaverage.lh
(MRIread)

I am getting that error because the fmcpr.brainmask.fsaverage.lh does 
not exist. To fix this error, I re-ran preprocessing using the 
following tutorial: *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc 
 



After preprocessing, I still got the same error.

*Here are the files that do exist in that path: 
*subnum/bold/run-num/masks* *
brain.e3.nii.gz            brain.fsaverage.lh.pr.nii.gz 
 brain.fsaverage.rh.pr.nii.gz  brain.mni305.2mm.pr.nii.gz 
 brain.nii.gz.mkbrainmask.log
brain.fsaverage.lh.nii.gz  brain.fsaverage.rh.nii.gz     
brain.mni305.2mm.nii.gz     brain.nii.gz


*There are some fmcpr files in this folder: subnum/bold/run-num*
fmcpr.brainmask.norm.2x2x2.nii.gz     fmcpr.mcdat fmcpr.norm.nii.gz 
 fmcpr.sm5.fsaverage.rh.nii.gz
fmcpr.brainmask.normtmp.2x2x2.nii.gz  fmcpr.nii.gz       
 fmcpr.sm0.norm.nii.gz  fmcpr.sm5.mni305.2mm.nii.gz
fmcpr.mat.aff12.1D      fmcpr.nii.gz.mclog 
 fmcpr.sm5.fsaverage.lh.nii.gz  fmcpr.sm5.norm.nii.gz



*Here are the commands I am running:*
*mkanalysis-sess*-fsd bold -rlf $analysis_stem-$run_set.rlf -surface 
fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 
-nconditions $nconditions -mask $func_stem.brainmask -gammafit 2.25 
1.25 -nuisreg mcprextreg 6 -TR 1. -polyfit 1 -analysis 
$analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM 
-tpexclude $tpe$TPE_STEM -funcstem 

Re: [Freesurfer] editing the aseg.mag using another tool and then rerunning

[Douglas N. Greve]

On 11/29/2021 11:55 AM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

A quick question.

Is it feasible or even possible to edit the aseg.mgz  using another 
program (i.e. ITK-snap after converting to nifti), and rerunning the 
pipeline using the revised aseg as input


To regenerate volumes and surfaces?

I think that should work. Edit the aseg.presuf.mgz, then run 
-autorecon2-noaseg -autorecon3


Do WM edits need to need to be completed on the WM.mgz and/or using 
Control Points?


I'm not sure what you mean here. WM edits can only be done on wm.mgz (or 
filled.mgz for 7.2+).


Jim



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Re: [Freesurfer] Hippocampal subfield data

[Iglesias Gonzalez, Juan E.]

It could be that your memory allocation is right on the edge of the 
requirements, and some subjects go over the bounds while others do not. Is it a 
possibility to allocate more RAM for your jobs?
Cheers,
/E

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

On Dec 10, 2021, at 14:35, Taylor, Lisa 
mailto:ltayl...@hs.uci.edu>> wrote:

External Email - Use Caution

Hi Juan,

Thank you.

I don't believe so. I reran freesurfer on this participant with another 
participant on the same day on our HPC. This participant did not populate the 
data while the other did populate the data, so I am not sure if there is 
something innate with the scan that is causing the problem, or something else?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Sent: Friday, December 10, 2021 11:22 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Hippocampal subfield data

Dear Lisa,
Is it possible that you’re running out of RAM memory? How much RAM do you have 
available?
Cheers,
Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com

On Dec 10, 2021, at 14:19, Taylor, Lisa 
mailto:ltayl...@hs.uci.edu>> wrote:

External Email - Use Caution

Hi,

Any reason why my participant is not creating hippocampal subfield data?

Thank you

Lisa



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viruses. The sender therefore does not accept liability for any errors or 
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transmission.

Re: [Freesurfer] Hippocampal subfield data

[Taylor, Lisa]

External Email - Use Caution

Hi Juan,

Thank you.

I don't believe so. I reran freesurfer on this participant with another 
participant on the same day on our HPC. This participant did not populate the 
data while the other did populate the data, so I am not sure if there is 
something innate with the scan that is causing the problem, or something else?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Friday, December 10, 2021 11:22 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal subfield data

Dear Lisa,
Is it possible that you’re running out of RAM memory? How much RAM do you have 
available?
Cheers,
Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1EpssHTdnx136bsFlaSi2FeYOAwdlljBBEhbBdpUCnjuo8fl9kzTObVgwQ9GuN8a9wr7kI3zGBD92CpanB2FTduohODSBI8k2v2wdFCgc1w2rzRpli0IfY0xK7wumSn3E5Llj6QtfZits7l9vj62DQ_mtJ0Do1X2isxNTlcS-0za7O-WktPdGBGbDowYeD1nniKugJAuwsaNkadYzQU1fvHTWjhpHDbPpYnUj9cCb3PdZ18OxlREZv45SJLVCOMxSzsOl6wG0GnA3obs6RNV9-eyAT_Kx9ofOGQtxwE3iWDMS3oPaWnzAg7bybINIZRSD/http%3A%2F%2Fwww.jeiglesias.com

On Dec 10, 2021, at 14:19, Taylor, Lisa 
mailto:ltayl...@hs.uci.edu>> wrote:

External Email - Use Caution

Hi,

Any reason why my participant is not creating hippocampal subfield data?

Thank you

Lisa



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Re: [Freesurfer] Hippocampal subfield data

[Iglesias Gonzalez, Juan E.]

Dear Lisa,
Is it possible that you’re running out of RAM memory? How much RAM do you have 
available?
Cheers,
Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Dec 10, 2021, at 14:19, Taylor, Lisa 
mailto:ltayl...@hs.uci.edu>> wrote:

External Email - Use Caution

Hi,

Any reason why my participant is not creating hippocampal subfield data?

Thank you

Lisa



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viruses. The sender therefore does not accept liability for any errors or 
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Re: [Freesurfer] Fieldmap Images in Nifti Format

[Yendiki, Anastasia]

Hi Elizabeth - From your log file, I see that you're using FreeSurfer 6. Please 
use the latest version (7.2), as TRACULA has undergone a drastic overhaul in 
this version. The TRACULA tutorials and documentation on the wiki apply to this 
new version.

To use field maps, you need one more acquisition parameter: the TE difference 
between the phase maps of the field mapping sequence. If the field map is in 
DICOM format, this parameter can be read from the header. If the field map is 
in NIfTI format, you have to specify this parameter manually in the config file 
(set dTE = ...)

BTW, if your data are in BIDS format, there is a new script that can figure all 
this stuff out and auto-generate the TRACULA config file:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71565.html

Hope this helps,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kaplan, Elizabeth 

Sent: Thursday, December 9, 2021 11:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Fieldmap Images in Nifti Format


External Email - Use Caution

Hi All,

I am working on processing diffusion data with Tracula and am running into an 
error when attempting to use fieldmaps to compensate for B0 inhomogeneity 
distortions. The error that I run into reads "ERROR: must specify as many 
gradient vector tables as DWI scans ". I am able to completely run Tracula 
processing when specifying dob0 = 0.

Is it possible to use fieldmap images that are in Nifti format or is DICOM 
format required for this input? Any other guidance is greatly appreciated!


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[Freesurfer] PhD position

[Dídac Vidal]

External Email - Use Caution

At the Center for Lifespan Changes in Brain and Cognition, University of
Oslo, Norway, we have an available PhD fellowship for a candidate highly
interested in applying longitudinal, multimodal models on neuroimaging data
and its relation to genetics and cognition to understand the brain
foundations for episodic memory preservation and loss in older age



The application deadline is: 16.01.2022

Please see more info here:
https://secure-web.cisco.com/1wnEXnVTSaJxvqRbBY18QbYibaL9-BHWSM5gMKGsdW_VLEHg65ZqBeTrBVwgeRihCpg9nN6Ipl_a197YvYueq93SHqmDBYqSroGEJil7tQeRA8reCaKPH9TXhdPA9RvoJhoJkbORW-JZlVfRRQ2TM43dhDW1uOYODATehyYLKb1j3TDOcyI0OhxHYqAXMj4i7RlVvR5yQpQWnoaf5NrGesyPe3iLVT-A_6RkRDeS-JUEPtEo6zJEIcUARRJeQzOumVPuWeLr36dnB6dNDopHU-pKbg88ElEnZXMqXqOaGxffQzo9Bq0i-ykvkZ8zkTOuM0DLv61vn2toDZ-lxDuVaJw/https%3A%2F%2Fwww.jobbnorge.no%2Fen%2Favailable-jobs%2Fjob%2F216380%2Fphd-fellowship-in-neuroimaging




P.S. Interested candidates are welcome to contact Didac Vidal-Pineiro (
d.v.pine...@psykologi.uio.no)



All the best,

Dídac

-- 
Dídac Vidal Piñeiro
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