Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Ting Li]

External Email - Use Caution

Hi experts, 

I have extracted the area of the significant cluster with the command like the 
following:
mri_segstats --i mgh/lh.volume.all.mgh  --seg 
glmdir_az_vz/lh.volume.all.glmdir/av-group2-vs-group2/cache.th20.neg.sig.ocn.mgh
 --id 1  --sumwf group1_group2_volume_l.sum-clusters.dat

When I use a t-test for these two group summarized area value, the p value is 
0.1398. I did the same process for other significant clusters. However, it is 
the only one without significant p-value. The detail of the cluster information 
is listed below. 

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxsWghtVtx   Annot

   1   -4.773   53922   1279.30-32.98.5   55.3  0.00300  0.00200  
0.00400   2126-5375.69  caudalmiddlefrontal

Could you give me some ideas where I should find the reason? Thanks a lot!

Regards,
Ting 
> On Aug 14, 2018, at 10:51 AM, Douglas Greve  wrote:
> 
> mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf 
> P2P3.means-in-clusterN.dat

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Re: [Freesurfer] mri_label2label dependencies

[Douglas N. Greve]

Hi Don, sorry for the delay. It is using the talairach.xfm files in both 
subjects to do the mapping.
doug

On 08/24/2018 11:40 AM, Krieger, Donald N. wrote:
>
> External Email - Use Caution
>
> Dear freesurfers,
>
> I didn’t see a response to this but I might have missed it.
>
> In any case it looks like it’s working ok.
>
> I found an error in what I was doing which was confusing things.
>
> Best – Don
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  *On Behalf Of *Krieger, Donald N.
> *Sent:* Wednesday, August 22, 2018 8:35 PM
> *To:* 'freesurfer@nmr.mgh.harvard.edu' 
> *Subject:* [Freesurfer] mri_label2label dependencies
>
> *External Email - Use Caution *
>
> Dear freesurfers,
>
> I am using mri_label2label with –regmethod volume .
>
> The only other switches I am using are minimal as you can see below.
>
> The thing is that none of the freesurfer stuff is in the srcsubject’s 
> directory.
>
> Why is there no error message?
>
> Where is it getting the stuff below the line: Src2TrgVolReg: 
> ---   ?
>
> Actually, I just need to know what to put into those directories so 
> this function will work properly.
>
> I see from the documentation that I need mri/transforms/talairach.xfm 
> in both the src and trg subject directories.
>
> Is there anything else that needs to be there?
>
> mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel 
> /dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume
>
> srclabel = /dev/shm/32089_tmp0-2
>
> srcsubject = subNo1
>
> trgsubject = 174
>
> trglabel = /dev/shm/32089_labels
>
> regmethod = volume
>
> usehash = 1
>
> Use ProjAbs  = 0, 0
>
> Use ProjFrac = 0, 0
>
> DoPaint 0
>
> SUBJECTS_DIR /usr/local/pkg/freesurfer//subjects
>
> FREESURFER_HOME /usr/local/pkg/freesurfer/
>
> Loading source label.
>
> Found 33 points in source label.
>
> Starting volumetric mapping 33 points
>
> Src2TrgVolReg: -
>
> 0.963  -0.002  -0.044   0.330;
>
> 0.034   0.930  -0.328  -0.544;
>
> 0.044   0.285   0.919   13.268;
>
> 0.000   0.000   0.000   1.000;
>
>   0  55. 17. 23.    52.2444 9.6043 41.6544
>
>   1  47. 1. 39.    43.8696 -10.7903 51.4429
>
>   2  52. -4. 28.    49.1826 -11.6594 40.1300
>
>   3  55. 17. 16.    52.5536 11.8998 35.2230
>
>   4  50. -10. 23. 47.4912 -15.6659 33.7380
>
> Writing label file /dev/shm/32089_labels 33
>
> mri_label2label: Done
>
> Thanks - Don
>
>
>
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Re: [Freesurfer] Designing Constrats for 3 Group 1 Covariate Analysis

[Douglas N. Greve]

Have you looked at this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
You should be able to generalize the two groups, one covariate, to three 
groups


On 08/24/2018 01:06 PM, O'Dell, Ryan wrote:
>
> External Email - Use Caution
>
> Dear freesurfers,
>
>
> I have what is likely a basic question but I'm new not only to 
> FreeSurfer but contrast matrix design and group analysis as well, and 
> was hoping for some help/clarification.
>
>
> Basically I want to run a GLM on our structural/functional data in 
> order to determine if there's any significant correlation between 
> cortical thickness and cortical amyloid deposition (measured by PiB), 
> factoring in any potential effects of APOE genotype (e3e3, e3e4, 
> e4e4). This means I want to construct an FSGD file with a 3 groups 
> (the 3 APOE genotypes) and 1 covariate (our calculated cortical 
> composite PiB value) for this analysis. However, I'm struggling with 
> the proper contrast designs which test the various hypotheses in such 
> a setup.
>
>
> Any answers, thoughts, or insights would be greatly appreciated. I 
> know this type of analysis is also likely QDEC-able, but I think the 
> FSGD approach would be more beneficial for my understanding of 
> contrast matrix design. Please let me know if I've left out any 
> information that could potentially help clarify my question/request.
>
>
> Best,
>
>
> Ryan O'Dell MD/PhD
>
> PGY2 Psychiatry Resident, NRTP
>
> Yale University
>
>
>
>
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Re: [Freesurfer] Convert mgh to gii

[Douglas N. Greve]

You need to specify a surface
mris_convert -c cache.th13.pos.sig.cluster.mgh 
$FREESURFER_HOME/subjects/fsaverage/surf/lh.white 
cache.th13.pos.sig.cluster.gii

On 08/24/2018 03:18 PM, David.Mackarthy wrote:
>
> External Email - Use Caution
>
> Hi FS experts,
> I ran surface based analysis between two groups. The final output 
> "is cache.th13.pos.sig.cluster.mgh" I would like to convert this file 
> to gii format using "mris_convert" I tried:
>
> mris_convert 
> -c cache.th13.pos.sig.cluster.mgh cache.th13.pos.sig.cluster.gii
>
> Please what I am doing wrong?
> Thanks for help
> -Dev
>
>
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Re: [Freesurfer] smoothing only on cortex when using mris_preproc

[Douglas N. Greve]

Yes, that is what the cortex flag is for. mris_preproc should 
automatically use the cortex flag

On 08/25/2018 05:06 PM, Alon Baram wrote:
>
> External Email - Use Caution
>
> Hello,
>
> When smoothing with mri_surf2surf, it's possible to use the --cortex 
> flag to constrain the smoothing only to cortex (exclude the medial 
> wall and zero it out).
>
> Is there a way to tell mris_preproc to do the same (i.e to pass the 
> --cortex flag when it calls mri_surf2surf?
>
> thanks!
>
>
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Re: [Freesurfer] input to mris_preproc

[Douglas N. Greve]

You can just use mri_concat file1.mgh file2.mgh ... fileN.mgh --o stack.mgh

On 08/25/2018 05:03 PM, Alon Baram wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have a surface measure calculated for each of my subjects, which I 
> have already resampled and smoothed on fsaverage using mri_surf2surf, 
> i.e for each subject I run:
> mri_surf2surf --hemi  --s fsaverage --sval 
>  --fwhm  --cortex --tval 
> I now want to stack the outputs of the commands above, so that I can 
> give the stacked image as an input to PALM. I think I should use 
> mris_preproc for that, but I'm not sure if the subjects (the argument 
> after the --s flags) should be the original subjects or fsaverage - 
> given that my surface measures are already resampled to fsaverage.
>
> That is, I'm not sure if the correct command is (for 2 subjects)
>
> mris_preproc --out  --target fsaverage --hemi  
> *--s subj1 --s subj2* --is  --is 
> 
>
> *or *
>
> mris_preproc --out  --target fsaverage --hemi  
> *--s fsaverage --s fsaverage* --is  --is 
> 
>
> Thanks!
>
>
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Re: [Freesurfer] mri_gtmpvc for partial volume

[Douglas N. Greve]

Yes, you just need to have it in the right format. I've attached an example.

On 08/24/2018 04:48 PM, miracle ozzoude wrote:


External Email - Use Caution

Hello,

Can i specify a lookup table when using mri_gtmpvc? This is because I 
have a non-freesurfer segmentation (MALPEM) and i would like to 
perform partial volume on it without having to run freesurfer on the 
subject for PET analysis. I have a lookup table for the segmentation.


I know mri_gtmpvc expects (?.ctab) file from the segmentation however, 
it will require processing the subject with freesurfer and petsurfer. 
I only want to use the partial volume command. How do I make it use 
the lookup table i made rather than  ?.ctab file?


Thank you.

Best,
Paul


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# TissueTypeSchema 
#ctTType   0  unknown   0   0   00
#ctTType   1  cortex  205  62  780
#ctTType   2  subcort_gm  230 148  340
#ctTType   3  wm0 255   00
#ctTType   4  csf 120  18 1340
#ctTType   5  head150 150 2000
  0  Unknown   0   0   00   0
  2  Left-Cerebral-White-Matter  245 245 2450   3
  4  Left-Lateral-Ventricle  120  18 1340   4
  5  Left-Inf-Lat-Vent   196  58 2500   4
  7  Left-Cerebellum-White-Matter220 248 1640   3
  8  Left-Cerebellum-Cortex  230 148  340   2
 10  Left-Thalamus-Proper  0 118  140   2
 11  Left-Caudate122 186 2200   2
 12  Left-Putamen236  13 1760   2
 13  Left-Pallidum12  48 2550   2
 14  3rd-Ventricle   204 182 1420   4
 15  4th-Ventricle42 204 1640   4
 16  Brain-Stem  119 159 1760   3
 17  Left-Hippocampus220 216  200   2
 18  Left-Amygdala   103 255 2550   2
 24  CSF  60  60  600   4
 26  Left-Accumbens-area 255 165   00   2
 28  Left-VentralDC  165  42  420   3
 30  Left-vessel 160  32 2400   4
 31  Left-choroid-plexus   0 200 2000   4
 41  Right-Cerebral-White-Matter 245 245 2450   3
 43  Right-Lateral-Ventricle 120  18 1340   4
 44  Right-Inf-Lat-Vent  196  58 2500   4
 46  Right-Cerebellum-White-Matter   220 248 1640   3
 47  Right-Cerebellum-Cortex 230 148  340   2
 49  Right-Thalamus-Proper 0 118  140   2
 50  Right-Caudate   122 186 2200   2
 51  Right-Putamen   236  13 1760   2
 52  Right-Pallidum   13  48 2550   2
 53  Right-Hippocampus   220 216  200   2
 54  Right-Amygdala  103 255 2550   2
 58  Right-Accumbens-area255 165   00   2
 60  Right-VentralDC 165  42  420   3
 62  Right-vessel160  32 2400   4
 63  Right-choroid-plexus  0 200 2210   4
 72  5th-Ventricle   120 190 1500   4
 80  non-WM-hypointensities  164 108 2260   2
 85  Optic-Chiasm234 169  300   3
130  Air 147  19 1730   5
165  Skull   120 120 1200   5
172  Vermis  119 100 1760   2
174  Pons119 159 1000   3
257  CSF-ExtraCerebral60  60  600   4
258  Head-ExtraCerebral  150 150 2000   5
1001  ctx-lh-bankssts  25 100  400   1
1002  ctx-lh-caudalanteriorcingulate  125 100 1600   1
1003  ctx-lh-caudalmiddlefrontal  100  25   00   1
1005  ctx-lh-cuneus   220  20 1000   1
1006  ctx-lh-entorhinal   220  20  100   1
1007  ctx-lh-fusiform 180 220 1400   1
1008  ctx-lh-inferiorparietal 220  60 2200   1
1009  ctx-lh-inferiortemporal 180  40 1200   1
1010  ctx-lh-isthmuscingulate 140  20 1400   1
1011  ctx-lh-lateraloccipital  20  30 1400   1
1012  ctx-lh-lateralorbitofrontal  35  75  500   1
1013  ctx-lh-lingual  225 140 1400   1
1014  ctx-lh-medialorbitofrontal  200  35  750   1
1015  ctx-lh-middletemporal   160 100  500   1
1016  ctx-lh-parahippocampal   20 220  600   1
1017  ctx-lh-paracentral   60 220  600   1
1018  ctx-lh-parsopercularis  220 180 1400   1
1019  ctx-lh-parsorbitalis 20 100  500   1
1020  ctx-lh-parstriangularis 220  60  200   1
1021  

Re: [Freesurfer] create surface mesh from arbitrary volume?

[Douglas N. Greve]

Yes, you can use mri_binarize with the --surf output option

On 08/26/2018 08:22 PM, Russell Butler wrote:
>
> External Email - Use Caution
>
> hello, i would like to create a mesh, such as the one in surf/lh.pial, 
> using an arbitrary binary volume.
>
>
> i'm aware that freesurfer can convert the subcortical volume ROIs to 
> surfaces, does anyone know if this can be applied to an arbitrary 
> binary volume?
>
>
> i would like to replicate the script by Anderson Winkler (see below) 
> but instead of on subcortical aseg, on an arbitrary volume that i 
> supply. is this possible? thanks,
>
>
>     # Pre-tessellate
>     echo "==> Pre-tessellating: ${s}, ${lab0}"
>     ${FREESURFER_HOME}/bin/mri_pretess \
>            ${SUBJECTS_DIR}/${s}/mri/aseg.mgz ${lab} \
>            ${SUBJECTS_DIR}/${s}/mri/norm.mgz \
>  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz
>
>     # Tessellate
>     echo "==> Tessellating: ${s}, ${lab0}"
>     ${FREESURFER_HOME}/bin/mri_tessellate \
>  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz \
>            ${lab} 
> ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth
>
>     # Smooth
>     echo "==> Smoothing: ${s}, ${lab0}"
>     ${FREESURFER_HOME}/bin/mris_smooth -nw \
>  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \
>            ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}
>
>     # Convert to ASCII
>     echo "==> Converting to ASCII: ${s}, ${lab0}"
>     ${FREESURFER_HOME}/bin/mris_convert \
>            ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \
>  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc
>     mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \
>        ${SUBJECTS_DIR}/${s}/ascii/aseg_${lab0}.srf
>
>
>
>
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Re: [Freesurfer] MRIread error

[Douglas N. Greve]

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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Re: [Freesurfer] MRIread error

[Song, Da-Yea]

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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Re: [Freesurfer] MRIread error

[Douglas N. Greve]

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
>
> 
> Disclaimer:
>
>
> The materials in this e-mail are private and may contain Protected 
> Information. Please note that e-mail communication is not encrypted by 
> default. You have the right to request further emails be encrypted by 
> notifying the sender. Your continued use of e-mail constitutes your 
> acknowledgment of these confidentiality and security limitations. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying, distribution, or the taking of any action in 
> reliance on the contents of this information is strictly prohibited. 
> If you have received this e-mail in error, please immediately notify 
> the sender via telephone or return e-mail.
>
>
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[Freesurfer] MRIread error

[Song, Da-Yea]

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

--
Disclaimer:


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information is strictly prohibited. If you have received this e-mail in error, 
please immediately notify the sender via telephone or return e-mail.
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Re: [Freesurfer] error in longitudinal stream command

[Barletta, Valeria]

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-boun...@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
>
>
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[Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Shatil, Anwar Shahadat]

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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Re: [Freesurfer] LME Univariate pvalue inconsistent

[Martin Reuter]

Hi Xiaoyu, 

again (see also other email) you should not run left hemispheres on the
right. This could introduce a processing bias, especially when you
force all left to be healthy and right to be diseased (or vice-versa). 

Instead run your images normally and then for the univariate , simply
compute the diff between the left and right ROI's (always healthy -
diseased). Then do a normal GLM analysis on this signed difference. 

Best, Martin


On Tue, 2018-08-28 at 21:27 +, Wang, Xiaoyu wrote:
> External Email - Use Caution
> Hello Freesurfer Developers,
>  
> I’m attempting to use Univariate LME analysis to compare the
> symptomatic and asymptomatic hemispheres of early stage Parkinson’s
> disease patients.
>  
> I re-organized the data so that the symptomatic hemisphere is the
> left hemisphere and the Asymptomatic is the right (by flipping the
> orig.mgz before recon-all).
>  
> I followed the LME model tutorial for univariate on the freesurfer
> wiki and created my qdec.tabel.dat to have the same layout as in the
> example with group 1 as left hemisphere and group 2 as right
> hemisphere.
>  
> I have a design matrix to do a simple linear model containing a group
> by time interaction with the contrast of [0 0 0 1 0 0]
>  
> After running the F-test however, I noticed that the p-value was
> really inconsistent across atlases.
> I used multiple atlases and noticed that the p-value can be as low as
> 1.00E-30 for many structures.
> This is too good to be true especially since after sending the
> thickness value to a statistician she came back with values greatly
> different from mine.
> However, the Bhat values were similar.
>  
> Can someone give me a hint as to what is going on?
>  
> Xiaoyu
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Re: [Freesurfer] error in longitudinal stream command

[Martin Reuter]

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

[Martin Reuter]

Hi Xiaoyu, 

I don't think it makes sense to model the hemisphere each as a
different group. Do you mean different time point?

The problem is that left hemispheres are probably anatomically slightly
different than right hemispheres (on average in healthy people). 

I would run every subject only once, then do a x-hemi analysis (I think
there are tools for that, which try to keep stuff unbiased with respect
to the hemi) and then perform your statistic on that.

Since not all diseased hemispheres are on one side, it makes sense to
attach a sign to the x-hemi difference so that you always have, e.g.
healthy-diseased. Then simply do a GLM on that. 

Best, Martin


On Tue, 2018-08-28 at 22:18 +, Wang, Xiaoyu wrote:
>   
> Hello Freesurfer Experts,
>  
> I am trying to compare the left and right hemisphere of a group of PD
> patients with Mass-Univarate LME.
>  
> From what I can see in the wiki tutorial, the mris_preproc only
> assembles data from one hemisphere at a time, which is not very
> usefull if I am doing a hemisphere comparison where each hemisphere
> is a different group.
>  
> I am thinking of getting around this issue by flipping each subject
> time point so that the right hemisphere is on the left and adding it
> as a new timepoint.
> For example:
> S01_1    s01_base
> S01_1f  s01_base
> S01_2    s01_base
> S01_2f  s01_base
>  
> However, Can I still create the base file the same way using this?
>   recon-all -base  -tp  -tp  ... -all
>  
> also for the fsaverage, would make_average_subject still work?
>  
> Xiaoyu
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Re: [Freesurfer] Manually editing location of surface

[Diamond, Bram Ryder]

Hi Elena,


I've taken a look through the files you shared with us and can only find the 
complete subject directories for sub-90188_run-01_T1w and sub-90310. The 
subject directory for sub-01262 (and 209 other subjects) is empty. Could you 
please send another link with the subject directory for sub-01262?


Thanks,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Elena Nicole Dominguez 

Sent: Wednesday, August 22, 2018 3:01:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manually editing location of surface


External Email - Use Caution

The subject in particular is in their 90's. I have been seeing a similar 
occurrence in many of my other subjects as well. I will be attaching a link 
through google drive to share the subject I recently sent. 
(https://drive.google.com/a/uci.edu/file/d/1ZuekNGyEJ7gPbM3Yl3S8HeNMVLL60l0_/view?usp=sharing)

Thank you for your help in looking into this and please let me know what else 
is needed on my behalf.

[https://drive-thirdparty.googleusercontent.com/16/type/application/x-gzip] 
sub-01262.tar.gz


On Wed, Aug 22, 2018 at 8:44 AM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
wow, looks like a pretty serious failure (which we rarely see). If you
tar, gzip and ftp the entire subject dir for this subject we will take a
look

cheers
Bruce
On Tue, 21 Aug 2018, Elena Nicole Dominguez wrote:

>
> External Email - Use Caution
>
> Thank you for getting back to me. I am attaching an example of one of the 
> problems I am encountering.
>
> On Tue, Aug 21, 2018 at 8:57 AM Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>   Hi Elena
>
>   can you send us an image to show us what the issue is? The correct
>   intervention depends on why the surface is not correct.
>
>   cheers
>   Bruce
>   On Fri, 17 Aug 2018,
>   Elena Nicole Dominguez wrote:
>
>   >
>   > External Email - Use Caution
>   >
>   > Hello FreeSurfer Developers,
>   > On the tutorial it states that it is not possible to directly edit 
> the location of a surface.
>   > However, on the corresponding video posted onto the website the 
> gentleman mentions being able to
>   > accomplish this. I have been trying to locate the literature on how 
> to do this and have not been
>   > successful. I am using 
> 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c'
>   >
>   > I would kindly appreciate some help on locating any tutorials or 
> information available.
>   >
>   > Thank you for your help.
>   >
>   >___
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>
>
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> 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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Re: [Freesurfer] Seeing Parcels as volumes

[Bruce Fischl]

Hi Maedeh

try mri_aparc2aseg

cheers
Bruce


On Wed, 29 Aug 2018, Maedeh Khalilian wrote:



External Email - Use Caution

Dear Douglas Greve;
Thank you for your great help.I did what you said successfully.Now I have 
another question.
I have used "mri_divide_parcellation" to have more parcels.this command gives me a 
".annot" 
file.How can i change this file into a format such as .nii so i can see the 
volumes in Mricro?
Cheers
Maedeh,

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[Freesurfer] error in longitudinal stream command

[Barletta, Valeria]

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


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[Freesurfer] Saving the Results into the Original Space

[Maedeh Khalilian]

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Dear FreeSurfer experts,
How can I save the result of parcellation and segmentation into the original 
space?
I would appreciate any help.
Best regards,
Maedeh___
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[Freesurfer] Seeing Parcels as volumes

[Maedeh Khalilian]

External Email - Use Caution

Dear Douglas Greve;
Thank you for your great help.I did what you said successfully.Now I have 
another question.
I have used "mri_divide_parcellation" to have more parcels.this command 
gives me a ".annot"  file.How can i change this file into a format such as 
.nii so i can see the volumes in Mricro?
Cheers
Maedeh,___
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