Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Anastasia Yendiki]

Hi Elijah - I suggest looking at the axial diffusivity (AD) and radial 
diffusivity (RD) to help you interpret these results. These are the 
diffusivity parallel and perpendicular to the main budnle going through a 
voxel, respectively. Essentially, FA tells you how different the AD and RD 
are from each other, and MD tells you how big AD and RD are in aggregate.


Here are just a couple of all the possible scenarios that can lead to 
opposite FA/MD relationships:


AD increases, RD stays the same => MD increases, FA increases
AD stays the same, RD increases => MD increases, FA decreases

Hope this helps,

a.y

On Thu, 24 Mar 2016, Elijah Mak wrote:


Hi Freesurfer Community,
I recently used mri_segstats to extract FA and MD as suggested
here: http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at
some of the correlations between FA and MD in the same regions, and came
across a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001 

As I understand, a clear-cut interpretation especially with regards to FA
changes is not so easy!  But could someone discuss / speculate as to why FA
and MD could be positively correlated within the entorhinal WM region? That
was found separately within a group of a elderly healthy controls and a
group of dementia subjects.

Thank you for your time!

Best Wishes,
Elijah


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Re: [Freesurfer] Trac-all -path Segmentation error

[Anastasia Yendiki]

Hi Katherine - The dlabel/ directory is created during the -prep step, 
when the structural segmentation gets mapped from T1 to diffusion space. 
However bedpost may still run fine without the dlabel/ directory. It seems 
that the problem is fairly early in the -prep step. Any errors there?


Best,

a.y

On Wed, 23 Mar 2016, Katherine Damme wrote:


Hey Anastasia,


Although the bedpost appears to complete properly the dlabel/diff is not
being created during the bedp step. I am not sure how or why this error is
occurring. That would, it appears, definitely be the cause of the failure.
However, I am not getting an error during the prep or the bedpost stage, and
so I am still completely lost any advice would be deeply appreciated!

Thank you,

KD

On Wed, Jan 13, 2016 at 6:07 PM, Anastasia Yendiki
 wrote:

  Hi Katherine - Do the freesurfer segmentations look ok? What
  about the registration from structural to diffusion? You can
  inspect those quickly with:

  freeview dmri/dtifit_FA.nii.gz
  dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.3

  Hope this helps,
  a.y

  On Sun, 3 Jan 2016, Katherine Damme wrote:

First I should note that using the same scripts I
completed 52 participants successfully and am
currently trying to
batch process the newest 42 participants that are
only failing at the path level. Upon Visual
Inspection they all
appear normal (with the exception of the one
attached). After carefully comparing a random sample
of 5 from each
group images from the files that failed versus the
files that were successful, I found:

1. The range of values in the mean_ph1samples in the
successful ( i.e. -3.00 to 87.30 ) differed from the
failures
(i.e. -2 to 17) (the successful samples varied on
their high end from 50-114 but the failures were on
the 5-24
range)
2. The range of values in the mean_th1samples in the
successful ( -0.02 to 19.12) differed from the
failures
(-0.00267 to 7.176) (the successful samples varied
on their high end from 19-17 but the failures were
on the 3-10
range)
3. Some, but not all (2/5), mean_S0samples, had a
abnormal range in successful (0 to 19998.4) compared
to the
unsuccessful (0 to 709.96)

However, I understand that the diffusion units are
likely arbitrary and not sure these patterns will
hold in a
larger sample.

I know this is a lot of confusing information and so
in response to your question. After an initial
inspection
there are two types of output:
1. data that appears visually normal with a slightly
altered range.
  Should I be concerned about the range if all other
data looks fine?

2. data that appears visually normal with a normal
range and bizarre merged files.
  What do you think could be a cause of these odd
merged files?




On Tue, Dec 22, 2015 at 1:54 PM, Anastasia Yendiki
 wrote:

      Hi Katherine - Have you looked at any of the
intermediate images? Do they look normal?

      a.y

      On Mon, 21 Dec 2015, Katherine Damme wrote:

            Hello Everyone!

            It looks as though my prep and bedp
stages completed properly, but the prep stage ends
in a
            segmentation
            errror.

            See attached and let me know your
thoughts. I would prefer not to have to redo all
steps if
            possible!
            Thank you!




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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Elijah Mak]

Hi Kirstie,

Yes indeed there were 3 subjects at the bottom-left of the plot.

To account for PV, I eroded the boundaries using *-seg-erode 1* during the
*mri_segstats* stage, and this resulted in a few subjects with no data for
the WM entorhinal region (although these were saved as "0" in the .stats
file). Do people generally do this for DTI studies?

All good now.

Many thanks again, Kirstie.

Best Wishes,
Elijah
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Re: [Freesurfer] Cortical thickness average

[Sahil Bajaj]

Thanks a lot Elijah, I will give a try to this and will surely get back to
you if I had any issue.

Thanks again for the help.

Regards,
Sahil

On Thu, Mar 24, 2016 at 6:39 PM, Elijah Mak  wrote:

> Hi Sahil,
>
> I did something similar recently. I believe you can use mri_concat with
> the -mean option to create an average map of the group.
>
> Another option might be make_average_subject?
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject
>
> Best Wishes,
> Elijah
>
>
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>


-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Kirstie Whitaker]

Hi Elijah,

Is there any chance you could attach a scatter plot? My suspicious mind thinks 
either a) there are outliers who are doing odd things, or b) the FA values are 
very different to those in other regions and therefore the correlation with MD 
wouldn't be expected to be the same. 

Kx

Sent from my iPhone, please excuse any typos or excessive brevity

> On 24 Mar 2016, at 23:59, Elijah Mak  wrote:
> 
> Hi Alshikho,
> 
> Yes, I am sure :) Same sequence for everyone. 
> 
> Just to add. FA and MD were significantly negatively correlated for the other 
> regions including the fusiform, precuneus, hippocampus, thalamus, etc. 
> 
> So I am very curious about what could be going on with the ERC here?
> 
> Best Wishes,
> Elijah
> 
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Elijah Mak]

Hi Alshikho

,

Yes, I am sure :) Same sequence for everyone.

Just to add. FA and MD were significantly negatively correlated for the
other regions including the fusiform, precuneus, hippocampus, thalamus,
etc.

So I am very curious about what could be going on with the ERC here?

Best Wishes,
Elijah
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Alshikho, Mohamad J.]

Are you sure that all your DTI images have the same acquisition parameters?!!






From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Elijah Mak 
[fk...@medschl.cam.ac.uk]
Sent: Thursday, March 24, 2016 7:33 PM
To: Freesurfer support list
Subject: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Freesurfer Community,

I recently used mri_segstats to extract FA and MD as suggested here: 
http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at 
some of the correlations between FA and MD in the same regions, and came across 
a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001

As I understand, a clear-cut interpretation especially with regards to FA 
changes is not so easy!  But could someone discuss / speculate as to why FA and 
MD could be positively correlated within the entorhinal WM region? That was 
found separately within a group of a elderly healthy controls and a group of 
dementia subjects.

Thank you for your time!

Best Wishes,
Elijah

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Re: [Freesurfer] Cortical thickness average

[Elijah Mak]

Hi Sahil,

I did something similar recently. I believe you can use mri_concat with the
-mean option to create an average map of the group.

Another option might be make_average_subject?

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

Best Wishes,
Elijah
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Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

[Joseph Dien]

Doug, I see now what your concern was with just adjusting the beta weights.  
Since FSFAST is using a pseudo-mixed effects model, there is also a need to 
pass the cesvar statistics up to the second level.  How that might accommodate 
the derivative boost computation is not straightforward to me.  I need to 
understand better what fsfast is doing.  I was wondering if you could answer a 
couple questions about how cesvar is computed;

1) The cesvar computations in the fast_fratio.m function provided a good guide. 
 According to it:
cescvm = inv(C*inv(X'*X)*X'*Sn*X*inv(X'*X)*C’);
where Sn is the covariance matrix of the noise after the whitening (which is on 
by default).
cesvar=rvar./cescvm.

How is Sn computed?

2) I need to understand what fsfast is doing conceptually but I couldn’t 
reconcile the Thirion et al (2007) Equation #5 and the equations above, 
specifically the inclusion of the rvar term.  Can you throw some light on this?

I greatly appreciate your helpful tips and this amazing software that you have 
written.

Respectfully,

Joe


> On Mar 17, 2016, at 15:48, Joseph Dien  wrote:
> 
> I did more digging around and came up with a procedure.  Please let me know 
> if it would cause any problems.
> Looking at the contents of the X.mat files (which contain the predictors), it 
> appears that the betas are indeed arranged as c1 d1 c2 d2…
> I also found that isxconcat-sess requires the contrast output of 
> mkcontrast-sess so I can’t just bypass it.
> 
> So my thought is:
> 
> 1) run mkanalysis-sess with -spmhrf 1
> 2) run selxavg3-sess with the -no-con-ok flag to get the spmhrf1 betas 
> without bothering with the contrasts
> 3) run mkanalysis-sess with -spmhrf 0
> 4) run selxavg3-sess again but with the contrasts to get everything set up
> 5) read in the spmhrf1 betas with MRIread and compute the Calhoun derivative 
> boost with the beta values in mri.vol
> 6) use these values to compute the desired contrasts.  From my examination of 
> a sample ces.nii.gz file, a simple linear combination based on the contrast 
> weights is all that is needed.
> 7) replace the contents of the corresponding spmhrf0 ces.nii.gz files’ 
> mri.vol with these new values
> 8) write out the new ces.nii.gz files.
> 9) proceed with the analysis stream, using isxconcat-sess to set up the 
> second level analysis
> 
> So the question is, would this work?  Am I neglecting files other than 
> ces.nii.gz that would need to be modified?  or other fields in the mri data 
> structure?
> When you referred to writing “out a new volume” is this what you meant?
> 
> Thanks again for this help!
> 
> Joe
> 
> 
>> On Mar 15, 2016, at 17:32, Joseph Dien > > wrote:
>> 
>> oh duh!  Sorry, wasn’t thinking clearly.
>> Okay, I see how to generate the betas now.  I don’t even need to mess with 
>> the mkcontrast-sess command.
>> I just run selxavg3-sess with the -no-con-ok flag.
>> With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex.
>> With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex.
>> With 12 conditions, 12 more betas is exactly right.
>> So how do I know which of the betas is which?
>> I looked through the files and couldn’t find any labels.
>> I’m guessing the first twelve are the condition betas for "spmhrf 0".
>> If so, for "spmhrf 1", is it arranged as:
>> 
>> 1) c1 c2 c3…d1 d2 d3...
>> 
>> or
>> 
>> 2) c1 d1 c2 d2...
>> 
>>  (where d is the first derivative term)
>> 
>> also, when I asked you earlier about implementing this procedure, I had 
>> suggested reading the betas, computing the Calhoun, then generating new 
>> beta.nii.gz files with the new betas replacing the original spmhrf0 betas 
>> and then continuing with the regular analysis stream but you said it would 
>> result in invalid p-values.  Instead, you suggested:
>> 
>> "I was just thinking you could load the beta into matlab, make the
>> Calhoun computations on each condition, then compute the contrasts, then
>> write out the new volume”
>> 
>> can you expand on how one might “compute the contrasts” and “write out the 
>> new volume”?
>> 
>> Thanks again for this help!
>> 
>> Joe
>> 
>> 
>>> On Mar 15, 2016, at 12:43, Douglas N Greve >> > wrote:
>>> 
>>> The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
>>> 
>>> On 03/13/2016 10:29 PM, Joseph Dien wrote:
 After a long break, back to this…
 
 My goal is still to get the betas for the first and maybe second spm 
 hrf so I can calculate a Calhoun derivative boost measure.
 
 As a first step I ran:
 
 mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh 
 -fwhm 5 -event-related  -paradigm RPA1fix.par -nconditions 12 -spmhrf 
 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg 
 nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
 
 to use the SPM HRF with one 

[Freesurfer] FA and MD *positively* correlated within same regions ?

[Elijah Mak]

Hi Freesurfer Community,

I recently used mri_segstats to extract FA and MD as suggested here:
http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at
some of the correlations between FA and MD in the same regions, and came
across a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001

As I understand, a clear-cut interpretation especially with regards to FA
changes is not so easy!  But could someone discuss / speculate as to why FA
and MD could be positively correlated within the entorhinal WM region? That
was found separately within a group of a elderly healthy controls and a
group of dementia subjects.

Thank you for your time!

Best Wishes,
Elijah
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[Freesurfer] Cortical thickness average

[Sahil Bajaj]

Hello FreeSurfer community,

I calculated cortical thickness for 100 controls following the instructions
described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

So I have 100 lh.thickness.fsaverage.mgh, one for each subject. I was
wondering if there is any way to average the thickness over these 100
lh.thickness.fsaverage.mgh files to get one final lh.thickness.fsaverage.mgh

I am interested in calculating cortical thickness for 15 previously defined
ROIs, but I do not want to calculate 15x100 text files using mri_segstats
i.e. 15 text files for each subject and then average over those but I would
rather prefer to average over 100 lh.thickness.fsaverage.mgh files first
and then calculate thickness for each ROI to get 11 text files.

Any help would be really appreciated.

Thanks,
Sahil
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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[Freesurfer] ROI within subject

[Ji Won Bang]

Dear. Freesurfer experts.

Hi. How are you?

I have a question about making ROI.

This might be a naive question, but any input would be greatly appreciated.

I preprocessed scans per run, thus I have register.dof6.dat file inside all
run epi directories.

Then, I made ROIs per single subject based on the single subject's
functional contrast map using the command:

tksurfer replay06 lh inflated -curv -gray

I overlayed the single subject's contrast result sig.nii.gz (obtained from
3 runs) and the registration file in 1 run(register.dof6.dat in 1 among 3
runs), then I cut the plane and then flattenr the cortex, made ROI.

While trying to check the ROIs, I realized that this ROI seems to be
slightly different depending on which register.dof6.dat I use (I tried all
3 runs' register.dof6.dat when overlaying).
tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay
$DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg
$DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01

I thought ideally, this functional ROI should be the same across all runs
if thes register files are perfectly registering each functional sans to
anatomical scan.

Is this a usual way when people make ROI based on functional contrast map
per each subject?

The way I did in the past did not have this kind of problem because I did
motion correction as targetting the first EPI (aligning all images to the
first EPI) and then used only 1 (same) register.dat file..

Please share your idea with me.

Thank you very much.

Best,
Ji Won
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Re: [Freesurfer] whole hemisphere is yellow

[Douglas N Greve]

Can you give us more info about the design and the contrast you are 
testing? What does the uncorrected map look like?

On 03/24/2016 09:56 AM, Miracle Ozzoude wrote:
> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus 
> area in yellow for one of my results however, for the other it displayed the 
> entire hemisphere in yellow. Do I need to use the configure-- overlay? ‎Also, 
> when I tried to view the cluster summary for the entire hemisphere results, I 
> did not see a single cluster unlike, the cluster summary for the precuneus 
> results
>
> Sent from my BlackBerry 10 smartphone.
>Original Message
> From: Bruce Fischl
> Sent: Thursday, March 24, 2016 9:48 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
>
> if it's all yellow it means everything is significant. What threshold are
> you using?
> On Thu, 24 Mar 2016, Miracle Ozzoude wrote:
>
>> Hello Bruce,
>> No. This was after I ran the correction for multiple comparisons. Do I need 
>> to change the threshold too? My other results were fine. Thanks
>> Best,
>> Miracle
>>
>> Sent from my BlackBerry 10 smartphone.
>>   Original Message
>> From: Bruce Fischl
>> Sent: Thursday, March 24, 2016 8:45 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] whole hemisphere is yellow
>>
>>
>> Hi Miracle
>>
>> have you tried changing the thresholds? What kinds of values are you
>> seeing?
>>
>> Bruce
>> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>>
>>> hello doug,
>>> i performed a group analysis and after correction for multiple comparisons 
>>> when i tried to load the corrected clusters the whole hemisphere was 
>>> completely yellow. what should i do?
>>> Best,
>>> Miracle
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
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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.
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Fax: 617-726-7422

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Re: [Freesurfer] REPOST: registering longitudinal data to template

[Martin Reuter]

Hi Clara,

long_mris_slopes is for the 2 stage approach. It computes a linear fit 
(within each subject) across time (using the base space), then it maps 
the results to the template (fsaverage) and applies smoothing. It can 
compute rate (slope of linear fit) or some percent change measures, also 
the average across time.

mris_preproc is a tool to stack and map data to the global template 
(fsaverage) and apply smoothing etc. It does not perform any fitting.

Best, Martin

On 03/24/2016 12:44 PM, Clara Kühn wrote:
> Thank you, Martin! That clears things up a lot!
>
> Could you explain what the difference is between the commands 
> long_mris_slopes and mris_preproc? As far as I understand they give you a 
> different output. But what do they do differently in respect to mapping 
> longitudinal data?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "mreuter" 
> An: "Freesurfer support list" 
> Gesendet: Mittwoch, 23. März 2016 19:01:42
> Betreff: Re: [Freesurfer] REPOST: registering longitudinal data to template
>
> Hi Clara,
>
> 1) You'd create a different table for your time point with fsid being
> the longitudinal directories s1.long.sbase , no fsid-base column. then
> you can map and stack these using cross sectional commands (mris_preproc
> --qdec  ...)
> 2) You should use Qdec or glm_fit for cross sectional analysis
> 3) Yes, only for 2 stage model, so don't use it (for long you use LME
> anyway and for cross see 2))
> 4) that commands create a table with one entry for each subject
> (referring to the base), this is also for 2 stage model (the second
> stage works on a subject by subject basis)
> 5) the -qcache in recon all maps and smoothes surface data to the
> template, so that it is available later. You can do that even on the
> long runs, or you can just manually map ans smooth things with preproc.
> 6) A different preproc call using a fsgd file rather than a qdec table.
> see the glm_fit tutorial for these things.
>
> Best, Martin
>
> On 03/23/2016 12:28 PM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> I would like to analyze my longitudinal data also cross-sectionally at 
>> single time points. I am a little confused as to how to register my data to 
>> the template and smooth it accordingly.
>>
>> So far, I have registered my longitudinal data to my template to use in LMEs 
>> with this command:
>> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template 
>> --hemi lh --meas thickness --out lh.thickness.mg
>>
>> and then smoothed it with this command:
>> mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval 
>> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape
>>
>> (1) Do I have to do it once with a cross-sectional command and once with a 
>> longitudinal command?
>> (2) Should I do the cross-sectional analyses in QDEC or with LME?
>>
>> Now the question is what these other commands are for?
>>
>> (3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness 
>> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
>> years --qcache kids_template --sd $SUBJECTS_DIR
>> --> I understood this is only for Two-Stage-Models, is that correct?
>>
>> (4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out 
>> qdec/cross.qdec.table.dat
>>
>> (5) recon-all -s name -qcache -target  name_of_template
>>
>> (6) mris_preproc --fsgd gender_age.fsgd --cache-in 
>> thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out 
>> lh.gender_age.thickness.10.mgh
>>
>>
>> Please help clear up my confusion :)
>> Thanks in advance,
>> Clara
>>
>>
>>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] REPOST: registering longitudinal data to template

[Clara Kühn]

Thank you, Martin! That clears things up a lot!

Could you explain what the difference is between the commands long_mris_slopes 
and mris_preproc? As far as I understand they give you a different output. But 
what do they do differently in respect to mapping longitudinal data?

Cheers, Clara

- Ursprüngliche Mail -
Von: "mreuter" 
An: "Freesurfer support list" 
Gesendet: Mittwoch, 23. März 2016 19:01:42
Betreff: Re: [Freesurfer] REPOST: registering longitudinal data to template

Hi Clara,

1) You'd create a different table for your time point with fsid being 
the longitudinal directories s1.long.sbase , no fsid-base column. then 
you can map and stack these using cross sectional commands (mris_preproc 
--qdec  ...)
2) You should use Qdec or glm_fit for cross sectional analysis
3) Yes, only for 2 stage model, so don't use it (for long you use LME 
anyway and for cross see 2))
4) that commands create a table with one entry for each subject 
(referring to the base), this is also for 2 stage model (the second 
stage works on a subject by subject basis)
5) the -qcache in recon all maps and smoothes surface data to the 
template, so that it is available later. You can do that even on the 
long runs, or you can just manually map ans smooth things with preproc.
6) A different preproc call using a fsgd file rather than a qdec table. 
see the glm_fit tutorial for these things.

Best, Martin

On 03/23/2016 12:28 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I would like to analyze my longitudinal data also cross-sectionally at single 
> time points. I am a little confused as to how to register my data to the 
> template and smooth it accordingly.
>
> So far, I have registered my longitudinal data to my template to use in LMEs 
> with this command:
> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template 
> --hemi lh --meas thickness --out lh.thickness.mg
>
> and then smoothed it with this command:
> mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval 
> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape
>
> (1) Do I have to do it once with a cross-sectional command and once with a 
> longitudinal command?
> (2) Should I do the cross-sectional analyses in QDEC or with LME?
>
> Now the question is what these other commands are for?
>
> (3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness 
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
> years --qcache kids_template --sd $SUBJECTS_DIR
> --> I understood this is only for Two-Stage-Models, is that correct?
>
> (4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out 
> qdec/cross.qdec.table.dat
>
> (5) recon-all -s name -qcache -target  name_of_template
>
> (6) mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage 
> --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
>
>
> Please help clear up my confusion :)
> Thanks in advance,
> Clara
>
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the precuneus 
area in yellow for one of my results however, for the other it displayed the 
entire hemisphere in yellow. Do I need to use the configure-- overlay? ‎Also, 
when I tried to view the cluster summary for the entire hemisphere results, I 
did not see a single cluster unlike, the cluster summary for the precuneus 
results

Sent from my BlackBerry 10 smartphone.
  Original Message
From: Bruce Fischl
Sent: Thursday, March 24, 2016 9:48 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] whole hemisphere is yellow


if it's all yellow it means everything is significant. What threshold are
you using?
On Thu, 24 Mar 2016, Miracle Ozzoude wrote:

> Hello Bruce,
> No. This was after I ran the correction for multiple comparisons. Do I need 
> to change the threshold too? My other results were fine. Thanks
> Best,
> Miracle
>
> Sent from my BlackBerry 10 smartphone.
>  Original Message
> From: Bruce Fischl
> Sent: Thursday, March 24, 2016 8:45 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
>
> Hi Miracle
>
> have you tried changing the thresholds? What kinds of values are you
> seeing?
>
> Bruce
> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>
>> hello doug,
>> i performed a group analysis and after correction for multiple comparisons 
>> when i tried to load the corrected clusters the whole hemisphere was 
>> completely yellow. what should i do?
>> Best,
>> Miracle
>> ___
>> 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
>
>
> 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.
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>
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Re: [Freesurfer] whole hemisphere is yellow

[Bruce Fischl]

if it's all yellow it means everything is significant. What threshold are 
you using?
On Thu, 24 Mar 2016, Miracle Ozzoude wrote:

> Hello Bruce,
> No. This was after I ran the correction for multiple comparisons. Do I need 
> to change the threshold too? My other results were fine. Thanks
> Best,
> Miracle
>
> Sent from my BlackBerry 10 smartphone.
>  Original Message
> From: Bruce Fischl
> Sent: Thursday, March 24, 2016 8:45 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] whole hemisphere is yellow
>
>
> Hi Miracle
>
> have you tried changing the thresholds? What kinds of values are you
> seeing?
>
> Bruce
> On Wed, 23 Mar 2016, Miracle Ozzoude wrote:
>
>> hello doug,
>> i performed a group analysis and after correction for multiple comparisons 
>> when i tried to load the corrected clusters the whole hemisphere was 
>> completely yellow. what should i do?
>> Best,
>> Miracle
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> but does not contain patient information, please contact the sender and 
> properly
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Re: [Freesurfer] whole hemisphere is yellow

[Miracle Ozzoude]

Hello Bruce,
No. This was after I ran the correction for multiple comparisons. Do I need to 
change the threshold too? My other results were fine. Thanks
Best,
Miracle

Sent from my BlackBerry 10 smartphone.
  Original Message
From: Bruce Fischl
Sent: Thursday, March 24, 2016 8:45 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] whole hemisphere is yellow


Hi Miracle

have you tried changing the thresholds? What kinds of values are you
seeing?

Bruce
On Wed, 23 Mar 2016, Miracle Ozzoude wrote:

> hello doug,
> i performed a group analysis and after correction for multiple comparisons 
> when i tried to load the corrected clusters the whole hemisphere was 
> completely yellow. what should i do?
> Best,
> Miracle
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Regarding: oblique view

[Bruce Fischl]

HI Sampada

wow, something went terribly wrong. Can you post an image of the actual 
volume and maybe of the wm segmentation?


cheers
Bruce

On Thu, 24 Mar 2016, Dr Sampada Sinha 
wrote:



Hello Bruce,

The recon-all -autorecon2 process exited with the error. The lh inflated no fix 
image
is attached with this email. I am also, attaching the mri_info and 
recon_all.log with
this email. I am basically trying to calculate the lGI of  the participants. I 
was
having issues with lGI but, its sorted noe. Will appreciate if I can be guided 
by you
about how to fix this. I found the same kind of surface in another participants.

With thanks and regards,

Sampada

On Tue, Mar 22, 2016 at 10:41 PM, Dr Sampada Sinha  
wrote:
  Hello Bruce,
Thanks again for your prompt response. We have an official holiday here. Will
send the info on Thursday.

Thanks and regards,
Sampada
Predoctoral student
KGMU, Lko
India 

On haveay, March 2016, Bruce Fischl  wrote:
  I see

  if you have defects that large you should look at the
  inflated.nofix surface to see what they are.

  What is your voxel resolution?

  cheers
  Bruce

  On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

Thanks Bruce for your reply. I did run it thru'
recon-all. It went for more than 2
days and then exited with XL defect error (convex hull
was more than 14000 and vertex
size about 54000). So today I started by running the
recon-all in parts. I did not
find anything wrong with brainmask files after running
autorecon1. I am presently
running the autorecon-2 process. Will get back with the
surf files when this process
is over.
Thank you again for your reply and support.

Kind regards, 

Sampada

On Tuesday, March 22, 2016, Bruce Fischl
 wrote:
      sure. Have you tried running it through
recon-all? It may work fine
      On
      Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

      > Thanks Bruce for your reply. The acquisition
was oblique and the voxel
      size doesn't
      > conform to the 1mm cube isotropic. I am trying
to work on it and figure
      out a
      > solution. However, if I am not, hope its okay
to send you the nifti
      image.
      > Thanks and regards,
      >
      > Sampada
      >
      >
      >
      > Rnday, March 20, 2016, Bruce Fischl
 wrote:
      >       what do you mean by "adding" an oblique
angle? If you mean
      acquiring the
      >       data obliquely you should be fine as long
as the voxels are close
      to 1mm
      >       isotropic.
      >
      >       cheers
      >       Bruce
      >       On Sun, 20 Mar 2016, Dr Sampada Sinha
wrote:
      >
      >       > Dear freesurfer experts,
      >       > Does adding an oblique angle during
coronal or axial
      acquisitions of
      >       T1w
      >       > images lead to topographical errors
during mri_fix_topology
      process?
      >       >
      >       > Thanks and regards,
      >       >
      >       > Sampada
      >       >
      >       >
      >       >
      >       > --
      >       > Sampada Sinha
      >       >
      >       >
      >       >
      >       >
      >       >
      >       >
      >       >
      >       >
      >       >
      >       >
      >       >
      >       >
      >     
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      >
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      >       is
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sent to you in error
      and the
      >       e-mail
      >       contains patient 

Re: [Freesurfer] whole hemisphere is yellow

[Bruce Fischl]

Hi Miracle

have you tried changing the thresholds? What kinds of values are you 
seeing?

Bruce
On Wed, 23 Mar 2016, Miracle Ozzoude wrote:

> hello doug,
> i performed a group analysis and after correction for multiple comparisons 
> when i tried to load the corrected clusters the whole hemisphere was 
> completely yellow. what should i do?
> Best,
> Miracle
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] errors message in QAtools

[Lars M. Rimol]

Hi,

I'm running QAtools on a set of subjects processed with FS 5.3.0, and
consistently get this message when recon_checker is running:

Processing each subcortical label ...
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
etc.


*And in the recon_check file I notice several of my subjects have this
error message:*

ERROR: Recon-all steps missing in subject  status file

 Expected to see the following step(s):
#@# Remove Neck ti. 22. mars 15:02:33 +0100 2016
in the recon-all-status.log file before (line # 12):
--> CA Reg Inv



*I ran recon-all -all, and the recon-all log file seems to indicate neck
removal was peformed*; from recon-all.log:

 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z
/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca
nu_noneck.mgz

erasing everything more than 25 mm from possible brain
reading atlas
'/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'...
reading input volume 'nu.mgz'...
reading transform 'transforms/talairach.m3z'...
--
writing output to nu_noneck.mgz...
nonbrain removal took 0 minutes and 51 seconds.
#--
#@# SkullLTA ti. 22. mars 14:45:17 +0100 2016

 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz
/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull_2.lta



 === NUMBER OF OPENMP THREADS = 1 ===
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
--
reading 'nu_noneck.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7
total sample mean = 92.0 (1443 zeros)

spacing=8, using 3481 sample points, tol=1.00e-05...



Apart from this, the snapshots look ok (except for one subject I asked
about in a previous e-mail) and there are no outliers in any of the
subjects (according to QAtools).

Any idea why I get this error message?



Thank you!


sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital
7006 Trondheim,
Norway
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Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[R Edgar]

On 24 March 2016 at 04:15, Francis Tyson Thomas
 wrote:

> The issue I faced was after following all your instructions when I cam to
> the step of "make j4" it threw an error saying that it was not able to find
> -lcudart. And it looked like it was looking for it in "/usr/local/cuda/lib"
> when the directory itself didn't exist. I fixed this by editing another line
> in the configure.in file. I changed from CUDA_LIBS="-L$CUDA_DIR/lib
> $LIB_CUDA -lcudart" to CUDA_LIBS="-L$CUDA_DIR/lib64 $LIB_CUDA -lcudart". Was
> this change right?

If it compiled and ran successfully, I think it was right. I'm not an
expert on autotools, and your machine might be laid out slightly
differently to mine.

> Also I noticed that the speedup wasn't extremely huge. The time for one
> recon-all run went down from 7 hrs 45 mins to 5hrs 20 mins. My understanding
> is that this is due to only certain modules being cuda-ised (if there is a
> word like that!) like the mri_ca_register  and the mri_em_register. Are
> there any other modules that are parallelized currently other than these?

em_register and ca_register were the only two I ported. I think that a
couple of the binaries on the surface side of things were accelerated
too, but I didn't do those. You are, indeed, encountering a practical
example of Amdahl's Law.

Currently, I'm still poking around mri_ca_register, since I think that
there's at least another minute which can be shaved off the runtime.
However, things are getting a little gnarly, since it appears that I
had the wrong mental model of how the datastructures fit together.

Feel free to ask any more questions,

Richard
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Re: [Freesurfer] Surface based analysis using FA maps

[Matt Glasser]

The point is that more than tissue damage will cause changes to FA.

Matt.

On 3/23/16, 9:17 PM, "Alshikho, Mohamad J."
 wrote:

>This is theoritically correct!
>If we do DTI to study the liver. How these measures can explain the
>tissue? It is not only white matter and gray matter!
>
>All DTI measures can explain how much space we have between the cells.
>More space means low FA and high RD. The opposit correct as well.
>Given that they share the same formula. If we accept RD as a marker for
>gray matter integrity. We should accept FA a marker for gray matter
>integrity.
>
>Yes I am looking for an optimal measure to evaluate tissue damage.
>
>Mohamad
>
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser
>[m...@ma-tea.com]
>Sent: Wednesday, March 23, 2016 9:29 PM
>To: Freesurfer support list
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>FA or fractional anisotropy explains the fraction of the diffusion that is
>along the long axis of the diffusion tensor.  In so far as the diffusion
>tensor is an accurate model of the underlying structural architecture,
>what you say might be true (e.g. in the small number of white matter
>regions with only one main fiber orientation).  Most of white matter has
>multiple fiber orientations and thus the diffusion tensor is not a great
>model.  In grey matter, the principle orientation of processes is radial
>to the surface (e.g. radial fibers, major dendrites), but there are are
>also tangential processes (e.g. Bands of Baillarger).  To get a decrease
>in FA, one could do a number of things:
>
>1) Decrease the strength of radial diffusion
>2) Increase the strength of tangential diffusion
>3) Decrease the strength of both radial and tangential diffusion
>
>Are you looking for a measure that shows tissue damage?
>
>Matt.
>
>On 3/23/16, 7:55 PM, "Alshikho, Mohamad J."
>malshi...@mgh.harvard.edu> wrote:
>
>>It can explain one thing "tissue integrity"
>>
>>It will tell us neurobiologically exactly what can tell us in tissues
>>other than the brain such as liver, lung, heart, joints,  etc
>>
>>Mohamad
>>
>>
>>-Original Message-
>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>>Sent: Wednesday, March 23, 2016 8:49 PM
>>To: Freesurfer support list 
>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>
>>Right but what do you think FA, MD, AD, RD, etc are telling you
>>neurobiologically in the grey matter?
>>
>>Matt.
>>
>>On 3/23/16, 7:18 PM, "Alshikho, Mohamad J."
>>>malshi...@mgh.harvard.edu> wrote:
>>
>>>Hi Matt,
>>>I highly appreciate your input on this!!
>>>
>>>Actually my goal is to study the difference in FA values between groups
>>>within the cortex. I know that diffusivities ( MD, AD and RD) can be
>>>used to evaluate gray matter and many people claim that it is much
>>>better to use diffusivities to evaluate gray matter But my interest is
>>>specifically in FA within the gray matter.
>>>
>>>For that reason I want to do surface based analysis to study the
>>>differences in FA between my study groups. I checked for the optimal
>>>ways to do it:
>>>1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
>>>2. And I found
>>>https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028
>>>109
>>>.html
>>>
>>>I ran the analysis using both methods.
>>>
>>>For the second method I replaced PET maps by FA maps and this was the
>>>reason for my question! If we can do the analysis that way using PET
>>>maps, why we can't do it using FA maps?
>>>
>>>I will be more than happy if you can suggest me an alternative approach
>>>to study FA on a surface.
>>>
>>>
>>>Best,
>>>Mohamad
>>>
>>>-Original Message-
>>>From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt
>>>Glasser
>>>Sent: Wednesday, March 23, 2016 8:04 PM
>>>To: Freesurfer support list 
>>>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>>>
>>>I too am puzzled as to why you would want to do this.  In terms of
>>>getting improvement in the alignment across subjects TBSS is one way to
>>>approach this.  Another would be to use the fiber orientations in the
>>>registration like these folks have done:
>>>http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage
>>>
>>>If you are interested in studying the properties of cortical grey
>>>matter there might be better modalities than FA.  If you can provide
>>>more details on what you are trying to do, perhaps that would clarify
>>>how to go about it?
>>>
>>>Peace,
>>>
>>>Matt.
>>>
>>>On 3/22/16, 2:49 PM, "Douglas N 

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[Francis Tyson Thomas]

Hi Richard,

That was really helpful. All the details were very clear and I was able to
get it up and running except for some small hiccups which I fixed with a
small hack.

The issue I faced was after following all your instructions when I cam to
the step of "make j4" it threw an error saying that it was not able to find
-lcudart. And it looked like it was looking for it in "/usr/local/cuda/lib"
when the directory itself didn't exist. I fixed this by editing another
line in the configure.in file. I changed from CUDA_LIBS="-L$CUDA_DIR/lib
$LIB_CUDA -lcudart" to CUDA_LIBS="-L$CUDA_DIR/lib64 $LIB_CUDA -lcudart".
Was this change right?

Also I noticed that the speedup wasn't extremely huge. The time for one
recon-all run went down from 7 hrs 45 mins to 5hrs 20 mins. My
understanding is that this is due to only certain modules being cuda-ised
(if there is a word like that!) like the mri_ca_register  and
the mri_em_register. Are there any other modules that
are parallelized currently other than these?

With regard to the code base I guess I'm also using the read-only git
repository of the main development trunk as per the instructions on the
freesurfer webpage.

Once again thank you very much for that detailed information.

Best,
Tyson


On Mon, Mar 21, 2016 at 6:47 PM, R Edgar  wrote:

> On 21 March 2016 at 19:59, Francis Tyson Thomas
>  wrote:
>
> > The first part was smooth. I got it done pretty quickly (installing CUDA
> and
> > setting it up!). However for the freesurfer portion I have two questions,
> >
> > 1. Bruce mentioned in another email thread that v6 beta should be out in
> a
> > week or so after testing is completed. Should I wait for that version,
> > assuming I get the source code for v6 when I download it as per the
> > instructions on the freesurfer page.
>
> Which version of the source code do you have access to? I'm using the
> read-only git repository of the main development trunk, sending
> patches back to Zeke, which he puts into CVS. I'm not sure which of
> those are making it over to v6.
>
> > 2. Also, would I have to compile and build all modules (mri_em_registe,
> > mri_ca_register etc or can I limit to just these two when I build it
> again.
>
> I imagine you'll have to run configure again. When you do, the key
> options you want are:
>  --enable-fermi-gpu --with-cuda="/usr/local/cuda"
> Note that on my machine:
> [rge21@cudastation ~]$ which nvcc
> /usr/local/cuda-7.5/bin/nvcc
> [rge21@cudastation ~]$ ls -alF /usr/local/cuda
> lrwxrwxrwx. 1 root root 8 Jan  9 16:30 /usr/local/cuda -> cuda-7.5/
> So if your CUDA installation went somewhere else, you'll have to
> adjust that --with-cuda path.
>
> Then when you compile, make sure the nvcc being used really is the one
> you've set (things will likely fail horribly if this isn't the case).
> If it isn't, you'll have to look in the configure file for:
>
> #
> # Nvidia CUDA enabling
> 
> CUDA_DIR=""
> with_cuda=""
>
> and then comment out
> # with_cuda=""
> or it will override the directory you set on the command line.
>
> Let me know if you need further help,
>
> Richard
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