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Today's Topics:
1. Repost: tracula stats including NAs? (Jacobs H (NP))
2. Re: Error viewing corrected results (Antonin Skoch)
3. MRI intensity normalize (shi yao wang)
4. Re: Error mri_surf2surf FS6 (Juergen Haenggi)
5. Error while attempting Segmentation (IPL Neurosurgery)
6. Re: Error while attempting Segmentation (Juergen Haenggi)
7. How to check if FS are processing correctly. (shi yao wang)
8. Re: Intensity normalization in longitudinal processing
(Bruce Fischl)
9. Re: MRI intensity normalize (Bruce Fischl)
10. -dura_thresh (Octavian Lie)
----------------------------------------------------------------------
Message: 1
Date: Fri, 10 Mar 2017 22:39:49 +0000
From: "Jacobs H (NP)" <
h.jacobs@maastrichtuniversity.nl>
Subject: [Freesurfer] Repost: tracula stats including NAs?
To: Freesurfer support list <
freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D4E8E959.31257%h.jacobs@maastrichtuniversity.nl>
Content-Type: text/plain; charset="us-ascii"
Hi FreeSurfer,
I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki).
In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter.
I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki).
Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ?
Look forward to your thoughts on this.
Best wishes
Heidi
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Message: 2
Date: Sat, 11 Mar 2017 00:09:40 +0100
From: Antonin Skoch <
ansk@ikem.cz>
Subject: Re: [Freesurfer] Error viewing corrected results
To:
freesurfer@nmr.mgh.harvard.eduMessage-ID: <
3114823440-24140@posta.medicon.cz>
Content-Type: text/plain; charset="utf-8"
Dear Sahil,
-approx tail and -twotail are completely different things:
-approx tail switch on the tail approximation which speeds up the permutations.
-twotail switch on two-sided hypothesis, without -twotail the hypothesis is only one-sided.
It is reassuring that you see some clusters in _tstat_fwep.mgz now. I think that this starts to make sense: Since without -twotail there was no value in clustere_tstat_fwep.mgz, I think that your setup without -twotail was testing the opposite one-sided hypothesis.
You have to decide which hypothesis you want to test. If you want to test one-sided hypothesis of negative correlation and use cluster forming threshold 0.05 (~ 1.3 in FreeSurfer -log10(p) convention), then I think you should invert sign of your contrast vector in Contrast.csv.
With one-sided hypothesis you can modify your cluster-forming threshold to qnorm(1-10^-1.3)=1.643704 to be consistent with the mri_glmfit-sim behaviour.
If you are testing two-sided hypothesis, your command line is I think almost OK, with following recommendations
When not using -approx tail, I would increase number of permutations at least to 5000.
Or add -approx tail and then you are running with tail approximation. Then you can retain -n 500 as Anderson recommended and your execution time would be much shorter.
To report on cluster by use mri_surfcluster, you can use the code snippet I send in some of my earlier mails. You can also get cluster-wise p-value by loading the *clustere_tstat_fwep.mgz into freeview and clicking on the cluster. You can get cluster area by clicking on particular cluster in clustere_tstat.mgz.
For visualization purposes Anderson mentioned that it is better to use -log10(p) (use the option -logp). Then you can interactively threshold your clusters according to the cluster-wise p-values (put 1.3 to min to hide clusters not significant at cluster-wise p=0.05).
Do not forget to apply Bonferroni correction on your p-values when you analyze both hemispheres.
To get *cope.mgz for the comparison, you should add -saveglm.
As for comparison of F.mgh and dpv_tstat.mgh: F should be (approximately?) square of _tstat at the same vertex, if your contrast vector has one row. The correspondence should be (almost?) exact in orthogonal design (as I wrote previously, I got exact correspondence in my testing orthogonal design). I am not sure for non-orthogonal but I think that this should approximately also correspond, so -2 in dpv_tstat.mgh and 12 in F.mgh in the same vertex is maybe OK, but I am not sure.
Antonin
Hi Antonin,
Just quick updates and few more points:
(A) Earlier, I was using "-approx tail" in my PALM command and I was not
getting any thing close to that big cluster but I noticed that you
mentioned '-twotail' in your last email. So I replaced "-approx tail"
with ''-twotail''
so the command I am running now is:
palm -i *.10.mgh -s fsaverage/surf/lh.white
fsaverage/surf/lh.white.avg.area.mgh
-d Xg.csv -t Contrast.csv -m mask.mgh -o Left_Hemi_results -C 1.95 -twotail
-n 500 -nouncorrected
and I found that I can see a cluster when I view *_culstere_tstat_fwep or
_dpv_tstat_fwep (both positive magnitude), which are very identical to
sig.mgh (negative magnitude) from mri_glmfit and big cluster of very high
negative PCC which I sent earlier.
Here, I am sending you a screen of *_culstere_tstat_fwep, *_dpv_tstat_fwep
and sig.mgh.
Could you please confirm if thats correct? If so, I have few more questions:
- When reporting about this cluster for publication, how can I find the
size, annotation etc. of this cluster?
- What 'min' and 'max' range of color bar would you recommend when
reporting *_culstere_tstat_fwep results for the best view possible (at p <
0.05)?
(B). Even though you said the matchings are valid for orthogonal design
only, still I just check quickly and found that:
1. Here, I could not find any file with name: *cope.mgh
2. Here, clusters between F.mgh and *dpv_tstat.mgh are very similar but
magnitude of dpv_tstat.mgh is very small and negative (~ -2) and of F.mgh
is very high and positive (~ +12)
3. Here, magnitude of sig.mgh is roughly same as *dpv_tstat_uncp.mgh: both
negative and similar big cluster (I am assuming that *dpv_tstat_uncp.mgh
represents uncorrected p here and is same as *dpv_tstat.mgh, somehow I do
not see *_uncp.mgh in my outputs).
Thanks a lot for Antonin,
Sahil
On Fri, Mar 10, 2017 at 1:58 AM, Antonin Skoch <
ansk@ikem.cz> wrote:
> Dear Sahil,
>
> thinking of that, the comparisons I suggested in previous mail are
> probably valid only for the case of orthogonal design. ?And even with the
> orthogonal design as Anderson said, the values can a bit differ:
>
>
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L= > FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=318728
>
> As I did my own tests with orthogonal design, the values were equal to the
> reasonable precision, apart from the case 3.
>
> So you could produce some testing orthogonal design and make similar tests
> on that.
>
> Antonin
>
>
>
> Dear Sahil,
>
> I would suggest at first to make check of your GLM PALM setup by comparing
> mri_glmfit and PALM output files (using the same design and contrast):
>
> 1. values of gamma.mgh should correspond to values of *cope.mgh
>
> 2. values of F.mgh should be (*dpv_tstat.mgh) ^2.
>
> 3. values of sig.mgh should be {roughly) values of
> -log10(*dpv_tstat_uncp.mgh) - I am currently not sure why I do not get
> exact correspondence here.
>
> 4. When you threshold the sig.mgh by some threshold in freeview (let it be
> x) and use the same corresponding cluster-forming z-score threshold -C ?in
> PALM computed as
>
> qnorm(1-10^-x/2)
>
> (and use two-sided hypothesis by specifying -twotail), your
> *clustere_tstat.mgz should show the clusters with the same shape
> (regardless of their values, the clusters will be defined by non-zero
> value, other vertices would be zero) as the thresholded display of sig.mgh
> (computed by -two sided hypothesis).
>
> If there is any inconsistence, then there is probably something wrong with
> your PALM setup.
>
> Antonin
>
>
> Dear Antonin,
>
> Could you please have a look at the attached screen shot. This map is with
> full number of permutations, without -approx tail -n 500 -nouncorrected
>
> Here, I noticed that its only *_dpv_tstat.mgz which looks correct and
> giving very high negative value, close to that big cluster, small positive
> values at red clusters and the value changes when I change the position of
> cursor.
>
> *_dpv_tstat_fwep shows value of 1 mostly but shows between 0.97 and 1
> close/at the red clusters and 1 elsewhere, even at the big blue negative
> cluster.
>
> Third, *_clustere_tstat_fwep and *_clustere_tstat shows 1 and 0
> respectively everywhere, even at the big blue negative cluster.
>
> If there is something fishy with the analysis, would you mind looking at
> the data and the detailed commands I am using to run the analysis?
>
> Thanks a lot,
> Sahil
>
> On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch <
ansk@ikem.cz> wrote:
>
> > Dear Sahil,
> >
> > to assure that there is no other issue with your setup, I would
> recommend to obtain cluster-wise p-pvalue of that big cluster to see if it
> is reasonable, i.e. if it is somewhat close to the significance.
> >
> > Therefore, I would load *_clustere_tstat_fwep and click to the area of
> big cluster and see what the values of the vertices in that region are.
> >
> > Or, I would increase --thmax in mri_surfcluster to see the cluster-wise
> p-value(s). If you use --thmax 0.9999 (or maybe 1), you should see
> cluster-wise FWER corrected p-values of all clusters formed by used
> cluster-forming threshold.
> >
> > I would also maybe try to switch-off tail approximation and run it in
> full number of permutations (i.e. do not use -approx tail -n 500
> -nouncorrected).
> >
> > If there is no other issue, then yes, the conclusion would be, that for
> the used cluster-extent inference and currently set cluster-forming
> threshold, none of the clusters survived FWER correction at cluster-wise
> p-value threshold of 0.05.
> >
> > Antonin
> >
> >
> >
> > Dear Antonin,
> >
> > Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any
> > significant cluster and similarly thresholded map *dpv_tstat.mgz also
> > doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like
> > even though there is big cluster but after FWER correction, the
> > significance goes away. Actually, even when I removed -logp, I still do
> not
> > see any significant cluster.
> >
> > Next, I tried to use mri_surfcluster using following three commands
> > following instructions from the link you sent:
> >
> > mri_binarize --i Results_Left_clustere_tstat_fwep.mgz --min 1 --o
> p_bin.mgz
> >
> > mris_calc --output pmap_filter.mgz Results_Left_clustere_tstat_fwep.mgz
> sub
> > p_bin.mgz
> >
> > mri_surfcluster --in pmap_filter.mgz --subject fsaverage --hemi lh
> --surf
> > white --annot aparc.a2009s --thmin 0.00000001 --thmax 0.05 --mask
> > glmdir/mask.mgh --sum summary --nofixmni
> >
> > This gives me 'zero' cluster in the summary file.
> >
> > If the above steps are correct, would you conclude that the LGI results
> are
> > not significant and un-reportable for publication purpose and I should
> give
> > a try to thickness, volume and area maps?
> >
> > Thanks you so much Antonin for all your help.
> > Sahil
> >
> >
> >
> > On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch <a...@ikem.cz> wrote:
> >
> > > Dear Sahil,
> > >
> > > If you used -logp as Anderson suggested, you should set your min to
> 1.3 to
> > > threshold your *_clustere_tstat_fwep map and see the clusters.
> > >
> > > What is the value of *_clustere_tstat_fwep in the region of the big
> > > cluster seen at thresholded map *dpv_tstat.mgz ? ?This should
> correspond to
> > > your -log10(p) of your cluster.
> > >
> > > I personally did not use -logp and use the mri_surfcluster for the
> > > reporting of the clusters, as I wrote in previous mail here:
> > >
> > >
freesurfer@nmr.mgh.harvard.edu > </msg52042.html"" target="_blank">
http://www.mail-archive.com/%3Ca%20href=>/msg52042.html"; title="
>
freesurfer@nmr.mgh.harvard.edu/msg52042.html"" title="
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html"" target="_blank">
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html";
> target="_blank">
freesurfer@nmr.mgh.harvard.edu" title="
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu" target="_blank">
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu > /msg52042.html
> >
> > >
> > > But it is only matter of personal preference.
> > >
> > > And, beware, that the LGI is very smooth measure, therefore also
> rather
> > > big cluster can be insignificant after FWER correction.
> > >
> > > Antonin
> > >
> > >
> > >
> > >
> > > Hi Antonin,
> > >
> > > Here, I am sending you more information:
> > >
> > > (1). I used following command:
> > > palm -i lh.Behav_LGI.10.mgh -s fsaverage/surf/lh.white
> > > fsaverage/surf/lh.white.avg.
> > area.mgh -d Xg_Behav.csv -t
> > > Contrast_Behav.csv
> > > -m lh.Behav_LGI.glmdir/mask.mgh -o Results_Left -Cstat extent -C 1.95
> > > -approx tail -n 500 -nouncorrected -logp
> > >
> > > (2). Somehow, view of *_clustere_tstat_fwep is single colored,
> thresholded
> > > 0 (min) and 1(max), which seems suspicious. Please find it attached.
> > >
> > > (3). Data showed in screen shot 1 is just partial correlation
> coefficient
> > > (PCC, limiting between 0.30-0.35), obtained after running glm_fit
> command
> > > and saved in glm directory.
> > >
> > > (4). *_clustere_tstat_fwep is attached here in this email.
> > >
> > > (5). If I load *dpv_tstat.mgz and threshold it between 1.3 (p = 0.05)
> and
> > > 2
> > > (max), I get the map attached 2nd in attached figure. I am not sure
> > > how to "threshold
> > > it by your cluster-forming threshold (I suppose that you should
> correctly
> > > convert z value to t-value), to see your initial clusters after
> > > thresholding".
> > >
> > > Thanks a lot Antonin.
> > > Sahil
> > >
> > >
> > >
> > > On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch <a...@ikem.cz> wrote:
> > >
> > > > Dear Sahil,
> > > >
> > > > could you send the full command-line and unthresholded view of
> > > > *_clustere_tstat_fwep ?
> > > >
> > > > How the data showed in screenshot 1 were produced?
> > > >
> > > > How are the actual p-values of your clusters in
> *_clustere_tstat_fwep?
> > > >
> > > > You can also use -saveglm and inspect the files containing values of
> GLM
> > > > fit.
> > > > You can load the *dpv_tstat.mgz file and threshold it by your
> > > > cluster-forming threshold (I suppose that you should correctly
> convert z
> > > > value to t-value), to see your initial clusters after thresholding.
> > > >
> > > > Regards,
> > > >
> > > > Antonin
> > > >
> > > >
> > > >
> > > > Thanks a lot Anderson and Antonin, that's really useful.
> > > >
> > > > Actually, I am having trouble in interpreting the results. Could you
> > > > please
> > > > share any document explaining all these tests/outputs and their
> > > > interpretation in simple terms?
> > > >
> > > > Here I am attaching a screen shot: (1) Simple partial correlations
> (I
> > > > adjusted the color bar between 0.30 and 0.35 to visualize the high
> > > > correlation coefficients, which is ~0.35) and (2) Results I get when
> I
> > > > used cluster
> > > > extent stats: *dpv_tstat
> > > > But I do not see any significant clusters when I view
> > > > *_clustere_tstat_fwep, *_dpv_tstat_fwep, which is very unexpected in
> my
> > > > data set.
> > > >
> > > > So basically I really doubt if I am running the stats correctly
> because
> > > > PCC
> > > > looks high at that big cluster (shown in PCC in attached screen
> shot).
> > > >
> > > > Could you please suggest if there is any alternative (less stronger)
> > > stat
> > > > flag I can use here while running PALM command?
> > > >
> > > > I would be more than happy sharing any required files to interpret
> the
> > > > results.
> > > >
> > > > Thanks.
> > > >
> > > > On Wed, Mar 8, 2017 at 10:20 AM, Sahil Bajaj <
sahil.br...@gmail.com>
>
> > > > wrote:
> > > >
> > > > > Thanks a lot Anderson and Antonin, that's really useful.
> > > > >
> > > > > Actually, I am having trouble in interpreting the results. Could
> you
> > > > > please share any document explaining all these tests/outputs and
> their
> > > > > interpretation in simple terms?
> > > > >
> > > > > Here I am attaching two screen shots: (1) Results I get when I
> used
> > > > cluster
> > > > > extent stats: *dpv_tstat and (2). Simple partial correlations (I
> > > > adjusted
> > > > > the color bar between 0.30 and 0.35 to visualize the high
> correlation
> > > > > coefficients, which is ~0.35).
> > > > > I do not see any significant clusters when I view
> > > *_clustere_tstat_fwep,
> > > > > *_dpv_tstat_fwep, which is very unexpected in my data set.
> > > > >
> > > > > So basically I really doubt if I am running the stats correctly
> > > because
> > > > > PCC looks high at that big cluster (shown in PCC in attached
> screen
> > > > shot).
> > > > >
> > > > > Could you please suggest if there is any alternative (less
> stronger)
> > > > stat
> > > > > flag I can use here while running PALM command?
> > > > >
> > > > > I would be more than happy sharing any required files to interpret
> the
> > > > > results.
> > > > >
> > > > > Thanks.
> > > > >
> > > > > On Wed, Mar 8, 2017 at 9:27 AM, Martin Juneja <mj70...@gmail.com>
> > > > wrote:
> > > > >
> > > > >> Hi Antonin and Anderson,
> > > > >>
> > > > >> That's wonderful ! I am able to run PALM now, without any
> problem.
> > > > >>
> > > > >> Thank you so much for your help and time, I really appreciate
> that.
> > > > >>
> > > > >> Best,
> > > > >> MJ
> > > > >>
> > > > >>
> > > > >>
> > > > >> On Wed, Mar 8, 2017 at 6:30 AM, Anderson M. Winkler <
> > > > >> wink...@fmrib.ox.ac.uk> wrote:
> > > > >>
> > > > >>> Hi all,
> > > > >>>
> > > > >>> That's exactly as Antonin says -- I have very little to add :-)
> > > > >>>
> > > > >>> Only a few suggestions:
> > > > >>>
> > > > >>> - With surfaces, both cluster and TFCE statistics tend to be
> slow.
> > > > >>> Consider using the tail approximation ("-approx tail -n 500
> > > > -nouncorrected")
> > > > >>>
> > > > >>> - Include -logp, so that the p-values are in log-10 scale.
> > > Significant
> > > > >>> p-values are then those above 1.3 (i.e., -log10(0.05). This will
> > > help
> > > > to
> > > > >>> make the figures nicer later.
> > > > >>>
> > > > >>> All the best,
> > > > >>>
> > > > >>> Anderson
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> On 8 March 2017 at 00:19, Antonin Skoch <a...@ikem.cz> wrote:
> > > > >>>
> > > > >>>> Dear Sahil,
> > > > >>>>
> > > > >>>> I suppose, for qcache 1.3 the equivalent cluster-forming
> threshold
> > > > >>>> z-value is
> > > > >>>>
> > > > >>>> two-tailed test:
> > > > >>>> qnorm(1-10^-1.3/2)=1.958949
> > > > >>>>
> > > > >>>> for one-tailed test:
> > > > >>>> qnorm(1-10^-1.3)=1.643704
> > > > >>>>
> > > > >>>> (qnorm is R function call for quantile function of normal
> > > > distribution,
> > > > >>>> you can compute this by using other methods or use statistical
> > > > z-tables)
> > > > >>>>
> > > > >>>> And, the directionality of the hypothesis is I suppose
> specified by
> > > > the
> > > > >>>> sign of your contrast vector, as I wrote in my previous mail.
> > > > >>>>
> > > > >>>> As for the output files, you can look at the documentation:
> > > > >>>>
> > > > >>>>
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide# > Output_files
> >
> > > > >>>>
> > > > >>>> For example, if you are looking for the p-values, used cluster
> > > extent
> > > > >>>> inference and used t-contrast, the file with FWER-corrected
> > > p-values
> > > > would
> > > > >>>> be something like
> > > > >>>>
> > > > >>>> output_basename_clustere_tstat_fwep.mgz
> > > > >>>>
> > > > >>>> Antonin
> > > > >>>>
> > > > >>>>
> > > > >>>>
> > > > >>>>
> > > > >>>> Hello Martin and Antonin,
> > > > >>>>
> > > > >>>> I was following this conversation very closely to understand
> how to
> > > > use
> > > > >>>> PALM in FreeSurfer.
> > > > >>>>
> > > > >>>> Can any of you please confirm in case I am interested in
> checking
> > > > >>>> correlation between gyrification index (LGI) and behavioral
> measure
> > > > using
> > > > >>>> two tailed, p < 0.05:
> > > > >>>> Step 1: I used --cache 1.3
> > > > >>>> Step 2: Because (1-10^-1.3)= 0.95, so I will have to use -C
> 0.95 in
> > > > palm
> > > > >>>> command
> > > > >>>>
> > > > >>>> Could you please confirm if thats correct and the output
> > > *_tstat.mgz
> > > > is the
> > > > >>>> final two-tailed corrected significant correlation map between
> LGI
> > > > and
> > > > >>>> behavioral data?
> > > > >>>>
> > > > >>>> Thanks a lot for this wonderful discussion.
> > > > >>>> Sahil
> > > > >>>>
> > > > >>>> PS: For one-tailed: it will be -C -0.95 in palm command,
> correct?
> > > > >>>>
> > > > >>>>
> > > > >>>>
> > > > >>>> On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch <a...@ikem.cz>
> > > wrote:
> > > > >>>>
> > > > >>>> > Dear Martin,
> > > > >>>> >
> > > > >>>> > after -s option, there have to be 2 arguments, as I specified
> in
> > > my
> > > > previous
> > > > >>>> > mail:
> > > > >>>> >
> > > > >>>> > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
>
> > > > >>>> >
> > > > >>>> > And beware that -C has to have negative sign, if your
> hypothesis
> > > is
> > > > >>>> > one-tailed negative.
> > > > >>>> >
> > > > >>>> > Antonin
> > > > >>>> >
> > > > >>>> >
> > > > >>>> >
> > > > >>>> > Hi Antonin,
> > > > >>>> >
> > > > >>>> > Thank you so much for this detailed explanation, that's
> really
> > > > useful.
> > > > >>>> >
> > > > >>>> > Following your instructions, I ran:
> > > > >>>> >
> > > > >>>> > palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh
>
> > >
> > > > -d
> > > > >>>> > check.csv -t Contrast_MEQ.csv -n 5000 -m
> > > lh.MEQ_LGI.glmdir/mask.mgh
> > > > -o
> > > > >>>> > myresults -Cstat extent -C 3.719016
> > > > >>>> >
> > > > >>>> > but I am getting following error:
> > > > >>>> >
> > > > >>>> > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with
> the
> > > > following
> > > > >>>> > options:
> > > > >>>> > -i lh.MEQ_LGI.10.mgh
> > > > >>>> > -s fsaverage/surf/lh.white.avg.area.mgh
> > > > >>>> > -d check.csv
> > > > >>>> > -t Contrast_MEQ.csv
> > > > >>>> > -n 5000
> > > > >>>> > -m lh.MEQ_LGI.glmdir/mask.mgh
> > > > >>>> > -o myresults
> > > > >>>> > -Cstat extent
> > > > >>>> > -C 3.719016
> > > > >>>> > Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh
> > > > >>>> > Reading input 1/1: lh.MEQ_LGI.10.mgh
> > > > >>>> >
> > > > >>>> > Struct contents reference from a non-struct array object.
> > > > >>>> >
> > > > >>>> > Error in palm_takeargs (line 1632)
> > > > >>>> > ? ? ? ? ? ? if any(size(plm.srf{s}.data.vtx,
> > > > >>>> > 1) == ...
> > > > >>>> >
> > > > >>>> > Error in palm_core (line 33)
> > > > >>>> > [opts,plm] = palm_takeargs(varargin{:});
> > > > >>>> >
> > > > >>>> > Error in palm (line 81)
> > > > >>>> > palm_core(varargin{:});
> > > > >>>> >
> > > > >>>> > Could you please help me in resolving this error?
> > > > >>>> >
> > > > >>>> > Thanks much.
> > > > >>>> >
> > > > >>>> > On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch <a...@ikem.cz>
> > > > wrote:
> > > > >>>> >
> > > > >>>> > > Dear Martin,
> > > > >>>> > >
> > > > >>>> > > input -i input file is
> > > > >>>> > >
> > > > >>>> > > lh.MEQ_LGI.10.mgh file in your glmdir directory (for left
> > > > hemisphere).
> > > > >>>> > >
> > > > >>>> > > As you could read in following messages in the referenced
> > > thread
> > > > in FSL
> > > > >>>> > > discussion forum, cluster-forming threshold need to be
> > > specified
> > > > in z, not
> > > > >>>> > > in t.
> > > > >>>> > >
> > > > >>>> > > Therefore, you would have to select cluster forming
> threshold
> > > and
> > > > specify
> > > > >>>> > > it as a z score.
> > > > >>>> > >
> > > > >>>> > > I think that your z-score for your original mri_glmfit-sim
> > > > commandline
> > > > >>>> > > argument
> > > > >>>> > >
> > > > >>>> > > --cache 4 neg
> > > > >>>> > >
> > > > >>>> > > will be ?-qnorm(1-10^-4)=-3.719016. (I am not perfectly
> sure
> > > > since I never
> > > > >>>> > > tried negative one-side hypothesis testing in PALM).
> > > > >>>> > >
> > > > >>>> > > You could also use other statistics, such as cluster mass,
> or
> > > > TFCE. See
> > > > >>>> > > PALM user guide.
> > > > >>>> > >
> > > > >>>> > > Do not include -pmethodp none and -pmethodr none, since you
> > > would
> > > > need the
> > > > >>>> > > partitioning due your non-orthogonal design matrix.
> > > > >>>> > >
> > > > >>>> > > ?h.white.avg.area.mgh file (which you will find under
> fsaverage
> > > > directory)
> > > > >>>> > > goes as second argument after -s option.
> > > > >>>> > >
> > > > >>>> > > Therefore I suppose the commandline for cluster extent
> > > inference
> > > > with
> > > > >>>> > > cluster forming threshold p=0.0001, negative one-sided
> > > > hypothesis, left
> > > > >>>> > > hemisphere, will be hopefully something like
> > > > >>>> > >
> > > > >>>> > > palm
> > > > >>>> > > -i y.mgh
> > > > >>>> > > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
>
> > >
> > > > >>>> > > -d Xg.csv
> > > > >>>> > > -t your_contrasts.csv
> > > > >>>> > > -n number_of_permutations
> > > > >>>> > > -m mask.mgh
> > > > >>>> > > -o output_basename
> > > > >>>> > > -Cstat extent
> > > > >>>> > > -C -3.719016
> > > > >>>> > > -saveglm
> > > > >>>> > > -savedof
> > > > >>>> > > -savemetrics
> > > > >>>> > >
> > > > >>>> > > The last 3 commandline options are only for diagnostical
> > > > purposes.
> > > > >>>> > >
> > > > >>>> > > The output is surface overlay you can visualize in
> freeview.
> > > > >>>> > >
> > > > >>>> > > I use following code snippet for the reporting significant
> > > > clusters in MNI
> > > > >>>> > > coordinates:
> > > > >>>> > >
> > > > >>>> > > # PALM output cluster extent p maps have 1 outside cluster
> -
> > > > problem with
> > > > >>>> > > mri_surfcluster and also for display in freeView
> > > > >>>> > > #here we set values 1 to 0 in pmaps.
> > > > >>>> > > #done by binarizing and subtracting
> > > > >>>> > > if [[ $# -ne 2 ]]; then
> > > > >>>> > > echo "get cluster summary of PALM statistics. Expecting 2
> > > > arguments: 1-
> > > > >>>> > > input p-map, 2- hemisphere (lh/rh)"
> > > > >>>> > > exit
> > > > >>>> > > fi
> > > > >>>> > > mri_binarize --i $1 --min 1 --o p_bin.mgz
> > > > >>>> > > mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz
> > > > >>>> > > mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject
> > > fsaverage
> > > > --hemi $2
> > > > >>>> > > --surf white --annot aparc --thmin 0.000000001 --thmax 0.05
> > > > --mask mask.mgh
> > > > >>>> > > --sum ${1%%.mgz}_cluster.summary --nofixmni
> > > > >>>> > > rm p_bin.mgz
> > > > >>>> > >
> > > > >>>> > > They are not Bonferroni-corrected for 2 hemispheres
> > > (--2spaces).
> > > > >>>> > >
> > > > >>>> > > Regarding your design and contrast:
> > > > >>>> > >
> > > > >>>> > > Design has to be matrix of values. You can use qdec to
> produce
> > > > Xg.dat file
> > > > >>>> > > with design matrix, then rename it to Xg.csv to be
> correctly
> > > > readable by
> > > > >>>> > > PALM.
> > > > >>>> > >
> > > > >>>> > > Regards,
> > > > >>>> > >
> > > > >>>> > > Antonin
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > > Hi Antonin,
> > > > >>>> > >
> > > > >>>> > > As you suggested in discussion forum, I tried to run
> following
> > > > command
> > > > >>>> > > after mri_glmfit:
> > > > >>>> > >
> > > > >>>> > > palm -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat
> > > > extent -C
> > > > >>>> > > 1.974975 -pmethodp none -pmethodr none -twotail -d
> > > Design_MEQ.txt
> > > > -t
> > > > >>>> > > Contrast_MEQ.txt
> > > > >>>> > >
> > > > >>>> > > Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a)
> with
> > > the
> > > > following
> > > > >>>> > > options:
> > > > >>>> > >
> > > > >>>> > > -s fsaverage/surf/lh.white
> > > > >>>> > >
> > > > >>>> > > -n 10000
> > > > >>>> > >
> > > > >>>> > > -m mask.mgh
> > > > >>>> > >
> > > > >>>> > > -Cstat extent
> > > > >>>> > >
> > > > >>>> > > -C 1.974975
> > > > >>>> > >
> > > > >>>> > > -pmethodp none
> > > > >>>> > >
> > > > >>>> > > -pmethodr none
> > > > >>>> > >
> > > > >>>> > > -twotail
> > > > >>>> > >
> > > > >>>> > > -d Design.txt
> > > > >>>> > >
> > > > >>>> > > -t Contrast.txt
> > > > >>>> > >
> > > > >>>> > > Found FSL in /usr/share/fsl/5.0
> > > > >>>> > >
> > > > >>>> > > Found FreeSurfer in /usr/local/freesurfer
> > > > >>>> > >
> > > > >>>> > > Found SPM in /usr/local/spm12
> > > > >>>> > >
> > > > >>>> > > Error using palm_takeargs (line 1141)
> > > > >>>> > >
> > > > >>>> > > Missing input data (missing "-i").
> > > > >>>> > >
> > > > >>>> > > Error in palm_core (line 33)
> > > > >>>> > >
> > > > >>>> > > [opts,plm] = palm_takeargs(varargin{:});
> > > > >>>> > >
> > > > >>>> > > Error in palm (line 81)
> > > > >>>> > >
> > > > >>>> > > palm_core(varargin{:});
> > > > >>>> > >
> > > > >>>> > > Looks like error is because its missing -i input here, I am
> not
> > > > sure what's
> > > > >>>> > > input file here?
> > > > >>>> > >
> > > > >>>> > > Also, I am trying to correlate LGI versus behavioral score,
> > > > regressing out
> > > > >>>> > > the effect of sex and age. So I just wanted to confirm if
> my
> > > > design.txt and
> > > > >>>> > > contrast.txt files are correct here. Please find both
> > > following:
> > > > >>>> > >
> > > > >>>> > > Design file (Variables Behav, Age) as following:
> > > > >>>> > >
> > > > >>>> > > S001 Male 60 36
> > > > >>>> > >
> > > > >>>> > > S003 Female 73 29
> > > > >>>> > >
> > > > >>>> > > S004 Male 48 39
> > > > >>>> > >
> > > > >>>> > > .......so on......
> > > > >>>> > >
> > > > >>>> > > Contrast file as following:
> > > > >>>> > > 0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit)
> > > > >>>> > >
> > > > >>>> > > Thank you so much for your help and time.
> > > > >>>> > >
> > > > >>>> > > On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja <
> > > mj70...@gmail.com>
> > > > wrote:
> > > > >>>> > >
> > > > >>>> > > > Hi Antonin,
> > > > >>>> > > >
> > > > >>>> > > > Thanks a lot for your reply.
> > > > >>>> > > >
> > > > >>>> > > > Somehow, in the link you sent, I could not find any
> response
> > > to
> > > > your
> > > > >>>> > > > email. But I can see your email to Anderson and command
> line
> > > > parameters.
> > > > >>>> > > >
> > > > >>>> > > > As I am not an expert in using FreeSurfer, so would it be
> > > > possible for you
> > > > >>>> > > > to share detailed step-by-step guide and PALM command
> after I
> > > > run
> > > > >>>> > > > mri_glmfit
> > > > >>>> > > > command and how and where to include
> '?h.white.avg.area.mgh'
> > > > file?
> > > > >>>> > > >
> > > > >>>> > > > I would really appreciate any help.
> > > > >>>> > > >
> > > > >>>> > > > On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch <
> a...@ikem.cz>
> > > > wrote:
> > > > >>>> > > >
> > > > >>>> > > >> Dear Martin,
> > > > >>>> > > >>
> > > > >>>> > > >> I think yes, you can use PALM with FreeSurfer surfaces,
> see
> > > my
> > > > >>>> > > >> conversation with Anderson on FSL list:
> > > > >>>> > > >>
> > > > >>>> > > >>
https://www.jiscmail.ac.uk/ > cgi-bin/webadmin?A2=ind1604&L=FSL
> > > > >>>>
> > > > >>>> >
> > > > >>>> > >
> > > > >>>> > > >> &D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088
>
> > >
> > > > >>>> > > >>
> > > > >>>> > > >> but beware not to forget to include average the vertex
> area
> > > > >>>> > > >> (?h.white.avg.area.mgh) file.
> > > > >>>> > > >>
> > > > >>>> > > >> Antonin
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >> If you don't have an orthogonal design, then you can't
> use
> > > > >>>> > > >> mri_glmfit-sim. I think you can use PALM:
> > > > >>>> > > >>
> > > > >>>> > > >>
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM > > > > >>>> > > >>
> > > > >>>> > > >> I have not tried it yet.
> > > > >>>> > > >>
> > > > >>>> > > >> Anderson, can you use PALM with surfaces?
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >> On 03/06/2017 05:23 PM, Martin Juneja wrote:
> > > > >>>> > > >> > Hi Dr. Greve,
> > > > >>>> > > >> >
> > > > >>>> > > >> > I tried to run: mri_glmfit-sim --glmdir
> lh.MEQ_LGI.glmdir
> > > > --sim perm
> > > > >>>> > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05
> > > > >>>> > > >> > It gives error that ERROR: design matrix is not
> > > orthogonal,
> > > > cannot be
> > > > >>>> > > >> > used with permutation.
> > > > >>>> > > >> >
> > > > >>>> > > >> > But when I run: mri_glmfit-sim --glmdir
> lh.MEQ_LGI.glmdir
> > > > --sim perm
> > > > >>>> > > >> > 1000 3 permcsd --sim-sign abs --cwpvalthresh .05
> > > > --perm-force, it
> > > > >>>> > > >> > works.
> > > > >>>> > > >> >
> > > > >>>> > > >> > I am not sure whether I will have to make the design
> > > matrix
> > > > >>>> > > >> > orthogonal. If so, could you please tell me how that
> can
> > > be
> > > > done?
> > > > >>>> > > >> >
> > > > >>>> > > >> > Or using --perm-force should be fine?
> > > > >>>> > > >> >
> > > > >>>> > > >> > Thanks.
> > > > >>>> > > >> >
> > > > >>>> > > >> > On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve
> > > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu <mailto:
> gr...@nmr.mgh.harvard <gr...@nmr.mgh.harvard>.
> > > edu
> > > > <gr...@nmr.mgh.harvard.edu>
> > > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu>
> > > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu>
> > > > >>>> > > >> > <gr...@nmr.mgh.harvard.edu>>> wrote:
> > > > >>>> > > >> >
> > > > >>>> > > >> > ? ? This is a problem with using LGI in that it is
> already
> > > > extremely
> > > > >>>> > > >> > ? ? smooth
> > > > >>>> > > >> > ? ? that the smoothness exceeds the limit of the look
> up
> > > > table that we
> > > > >>>> > > >> > ? ? supply. I ?recommend that you not use a
> gaussian-based
> > > > correction
> > > > >>>> > > >> > for
> > > > >>>> > > >> > ? ? LGI. Instead, use permutation (see mri_glmfit-sim
> > > > --help).
> > > > >>>> > > >> >
> > > > >>>> > > >> >
> > > > >>>> > > >> >
> > > > >>>> > > >> > ? ? On 03/06/2017 01:36 PM, Martin Juneja wrote:
> > > > >>>> > > >> > ? ? > Hello everyone,
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > I am trying to extract clusters showing
> significant
> > > > correlation
> > > > >>>> > > >> > ? ? > between LGI and a behavioral measure. I am able
> to
> > > > extract PCC
> > > > >>>> > > >> > and
> > > > >>>> > > >> > ? ? > sig.mgh but at the last step when I try to run
> > > > simulation command
> > > > >>>> > > >> > to
> > > > >>>> > > >> > ? ? > view corrected results and I run:
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir
> --cache 4
> > > > neg --cwp
> > > > >>>> > > >> > 0.05
> > > > >>>> > > >> > ? ? > --2spaces
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > I get following error:
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > ERROR: cannot find
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> >
> > > > >>>> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
>
> > > > cortex/fwhm35/neg/th40/mc-z.csd
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > But I can see mc-z.csd file in fwhm30 etc.
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > Full message on terminal window is attached
> > > following.
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > Any help would be really appreciated.
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > ----- Full message ----
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh
> --fsgd
> > > > MEQ.fsgd
> > > > >>>> > > >> > ? ? dods --C
> > > > >>>> > > >> > ? ? > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex
> > > --glmdir
> > > > >>>> > > >> > ? ? lh.MEQ_LGI.glmdir
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > WARNING: unrecognized mri_glmfit cmd option
> > > > mri_glmfit.bin
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > SURFACE: fsaverage lh
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log
>
> > >
> > > >
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > /usr/local/freesurfer/bin/mri_glmfit-sim
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp
> 0.05
> > > > --2spaces
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36
> greve
> > > > Exp $
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > Mon Mar ?6 11:11:13 MST 2017
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > setenv SUBJECTS_DIR
> > > > >>>> > > >> > ? ? > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll
>
> > >
> > > >
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > FREESURFER_HOME /usr/local/freesurfer
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > Original mri_glmfit command line:
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh
> --fsgd
> > > > MEQ.fsgd
> > > > >>>> > > >> > ? ? dods --C
> > > > >>>> > > >> > ? ? > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex
> > > --glmdir
> > > > >>>> > > >> > ? ? lh.MEQ_LGI.glmdir
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > DoSim = 0
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > UseCache = 1
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > DoPoll = 0
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > DoPBSubmit = 0
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > DoBackground = 0
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > DiagCluster = 0
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > gd2mtx = dods
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > fwhm = 35.073391
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? > ERROR: cannot find
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> >
> > > > >>>> > > >> > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
>
> > > > cortex/fwhm35/neg/th40/mc-z.csd
> > > > >>>> > > >> > ? ? >
> > > > >>>> > > >> > ? ? >
>
> _______________________________________________
> Freesurfer mailing list
>
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>
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Message: 3
Date: Fri, 10 Mar 2017 23:05:44 -0500
From: shi yao wang <
wangshiyao2009@gmail.com>
Subject: [Freesurfer] MRI intensity normalize
To:
freesurfer@nmr.mgh.harvard.eduMessage-ID:
<
CA+rJNW_1wctbHpCxhyEEkWzBdF9c6xtUF_Tt61jjLLy0HcZQxQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear FS experts,
I am wondering the process of MRI intensity normalization.
Before I am running recon -all, can I run following process to normalize
our MRI images.
mri_normalize SUBJECT/mri/nu SUBJECT/mri/wm
or any other preprocessing methods to avoid bias.
thanks
Lawrence
Emory University
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Message: 4
Date: Sat, 11 Mar 2017 10:50:31 +0100
From: Juergen Haenggi <
j.haenggi@psychologie.uzh.ch>
Subject: Re: [Freesurfer] Error mri_surf2surf FS6
To: Freesurfer support list <
freesurfer@nmr.mgh.harvard.edu>
Message-ID: <
C1F94AA7-C51A-4006-AC79-4C78C8102B01@psychologie.uzh.ch>
Content-Type: text/plain; charset="windows-1252"
Dear Douglas
thanks a lot for this information.
Indeed, I thought we are sampling our data on the own average!
Cheers
J?rgen
-----------------------------------------------------------------------------------------------------
University of Zurich
Dr. J?rgen H?nggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
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Am 09.03.2017 um 17:46 schrieb Douglas N Greve:
> This was done to clear up a misunderstanding when using a target subject
> other than fsaverage. The way that 5.3 worked is that the data were
> actually sampled onto fsaverage through the ?h.sphere.reg. The target
> subject was only used in the smoothing process (if you even specified
> that as part of mris_preproc). This gave people the impression that they
> were sampling their data onto the target subject. To replicate 5.3, just
> specify fsaverage as the target and proceed as normal using your target
> after those commands. If you want to sample onto your target subject,
> then you will have to register each individual subject to the target, eg,
>
> surfreg --s individualsubject --t average_AN_FS6_long_split
>
> This will create ?h.average_AN_FS6_long_split.sphere.reg which can then
> be used in mris_preproc
>
>
>
> On 03/09/2017 07:44 AM, Juergen Haenggi wrote:
>> Dear FS experts
>>
>> we are trying to run statistics in FS6 Linux. Everthing worked fine
>> until we applied the command
>> mris_preproc that called mri_surf2surf and produced the following error:
>>
>> #############################################################
>>
>> ---------------------------------------------------
>> #@# 1/98 s1006_01.long.s1006_base Thu Mar 9 13:20:16 CET 2017
>> --------------
>> -----------------------
>> mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh
>> --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject
>> average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval
>> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
>> --sval
>> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume
>> --jac --sfmt curv --noreshape --cortex
>> MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg):
>> could not open file
>> Source registration surface changed to
>> average_AN_FS6_long_split.sphere.reg
>> Target registration surface changed to sphere.reg
>>
>> $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $
>>
>> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
>> cd /usr/local/freesurfer/subjects
>> mri_surf2surf --srcsubject s1006_01.long.s1006_base --srchemi rh
>> --srcsurfreg average_AN_FS6_long_split.sphere.reg --trgsubject
>> average_AN_FS6_long_split --trghemi rh --trgsurfreg sphere.reg --tval
>> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
>> --sval
>> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume
>> --jac --sfmt curv --noreshape --cortex
>>
>> sysname Linux
>> hostname psy-neuro-clt-Monster
>> machine x86_64
>> user ego
>> srcsubject = s1006_01.long.s1006_base
>> srcval =
>> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.volume
>> srctype = curv
>> trgsubject = average_AN_FS6_long_split
>> trgval =
>> ./average_AN_FS6_long_split/stats/lme_preproc/tmp.mris_preproc.3575/s1006_01.long.s1006_base.1.mgh
>> trgtype =
>> srcsurfreg = average_AN_FS6_long_split.sphere.reg
>> trgsurfreg = sphere.reg
>> srchemi = rh
>> trghemi = rh
>> frame = 0
>> fwhm-in = 0
>> fwhm-out = 0
>> label-src = rh.cortex.label
>> label-trg = rh.cortex.label
>> OKToRevFaceOrder = 1
>> UseDualHemi = 0
>> Reading source surface reg
>> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg
>> No such file or directory
>> mri_surf2surf: could not read surface
>> /usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg
>> No such file or directory
>>
>> ###############################################################
>>
>> this line is odd:
>>
>> MRISread(/usr/local/freesurfer/subjects/s1006_01.long.s1006_base/surf/rh.average_AN_FS6_long_split.sphere.reg):
>> could not open file
>>
>> we are wondering why FS6 introduced the name of the target average
>> (average_AN_FS6_long_split) into the name of the individual subject
>> (rh.average_AN_FS6_long_split.sphere.reg) when looking
>> for s1006_01.long.s1006_base/surf/rh.sphere.reg.
>>
>> When using FS5.3.0 mris_preproc worked without this error.
>>
>> Any idea?
>>
>> Thanks in advance
>> Best regards
>> J?rgen
>>
>>
>> -----------------------------------------------------------------------------------------------------
>> University of Zurich
>> Dr. J?rgen H?nggi, Ph.D.
>> Department of Psychology
>> Division Neuropsychology
>> Binzmuehlestrasse 14, PO Box 25
>> 8050 Zurich, Switzerland
>>
>> 0041 44 635 73 97 (phone office)
>> 0041 76 445 86 84 (phone mobile)
>> 0041 44 635 74 09 (fax office)
>> BIN 4.D.04 (office room number)
>>
>>
j.haenggi@psychologie.uzh.ch <
mailto:j.haenggi@psychologie.uzh.ch> (email)
>>
http://www.psychologie.uzh.ch/neuropsy/ (website)
>>
http://www.juergenhaenggi.ch (private website)
>>
>> This e-mail (and any attachment/s) contains confidential and/or privileged
>> information. If you are not the intended recipient (or have received this
>> e-mail in error) please notify the sender immediately and destroy this
>> e-mail. Any unauthorised copying, disclosure or distribution of the
>> material in this e-mail is strictly forbidden.
>> -----------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>>
Freesurfer@nmr.mgh.harvard.edu>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
>
greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> _______________________________________________
> Freesurfer mailing list
>
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
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>
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Message: 5
Date: Sat, 11 Mar 2017 09:56:30 +0000
From: IPL Neurosurgery <
iplneuro@outlook.com>
Subject: [Freesurfer] Error while attempting Segmentation
To: "
freesurfer@nmr.mgh.harvard.edu" <
freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<
KL1PR0401MB2182761F90123D6D8B1C5ECDCA230@KL1PR0401MB2182.apcprd04.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
We have newly installed Freesurfer. We are a novice. We were trying to segment our data set. We used the following command. We attached the log.
Command: recon-all -s testsample -all
Output:
[iplneurosurgery@localhost /]$ recon-all -s testsample -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/iplneurosurgery/Documents/freesurfer/subjects
Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
-rw-rw-r--. 1 iplneurosurgery iplneurosurgery 18906 Mar 11 12:15 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.log
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
'/usr/local/freesurfer/bin/recon-all' -> '/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.local-copy'
#--------------------------------------------
#@# MotionCor Sat Mar 11 14:48:00 IST 2017
Found 1 runs
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample
mri_convert /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
mri_convert.bin /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-0.989525, -0.140773, -0.0319737)
j_ras = (0.144349, -0.962296, -0.230541)
k_ras = (0.00168578, -0.232741, 0.972537)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz...
mri_add_xform_to_header -c /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/transforms/talairach.xfm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Mar 11 14:48:05 IST 2017
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.10571
/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
i_ras = (-1, 9.77889e-09, 1.16415e-09)
j_ras = (5.82077e-09, 0, -1)
k_ras = (1.21945e-08, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.10571/nu0.mnc...
--------------------------------------------------------
Iteration 1 Sat Mar 11 14:48:07 IST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10571/nu0.mnc ./tmp.mri_nu_correct.mni.10571/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10571/0/ -iterations 1000 -distance 50
/home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
ERROR: nu_correct
Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s testsample exited with ERRORS at Sat Mar 11 14:48:07 IST 2017
freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform: Cent OS 7
uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sent from Outlook<
http://aka.ms/weboutlook>
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Message: 6
Date: Sat, 11 Mar 2017 11:02:28 +0100
From: Juergen Haenggi <
j.haenggi@psychologie.uzh.ch>
Subject: Re: [Freesurfer] Error while attempting Segmentation
To: Freesurfer support list <
freesurfer@nmr.mgh.harvard.edu>
Message-ID: <
9ED4F78F-2D4B-4AEA-97F0-9A38BC85FA8B@psychologie.uzh.ch>
Content-Type: text/plain; charset="iso-8859-1"
Hi IPL Neurosurgery
it seems that you have no read or write permission to the freesurfer tools.
> /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
you can change the permission with
sudo chmod -R 777 freesurfer
Hope this helps
Cheers
J?rgen
-----------------------------------------------------------------------------------------------------
University of Zurich
Dr. J?rgen H?nggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.
-----------------------------------------------------------------------------------------------------
Am 11.03.2017 um 10:56 schrieb IPL Neurosurgery:
> Hi,
>
> We have newly installed Freesurfer. We are a novice. We were trying to segment our data set. We used the following command. We attached the log.
>
> Command: recon-all -s testsample -all
>
> Output:
>
> [iplneurosurgery@localhost /]$ recon-all -s testsample -all
> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> INFO: SUBJECTS_DIR is /home/iplneurosurgery/Documents/freesurfer/subjects
> Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer
> -rw-rw-r--. 1 iplneurosurgery iplneurosurgery 18906 Mar 11 12:15 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.log
> Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
> /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
> '/usr/local/freesurfer/bin/recon-all' -> '/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.local-copy'
> #--------------------------------------------
> #@# MotionCor Sat Mar 11 14:48:00 IST 2017
> Found 1 runs
> /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
>
> cp /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz
>
> /home/iplneurosurgery/Documents/freesurfer/subjects/testsample
>
> mri_convert /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
>
> mri_convert.bin /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz...
> TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
> i_ras = (-0.989525, -0.140773, -0.0319737)
> j_ras = (0.144349, -0.962296, -0.230541)
> k_ras = (0.00168578, -0.232741, 0.972537)
> changing data type from short to uchar (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz...
>
> mri_add_xform_to_header -c /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/transforms/talairach.xfm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz
>
> INFO: extension is mgz
> #--------------------------------------------
> #@# Talairach Sat Mar 11 14:48:05 IST 2017
> /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
>
> mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
>
> /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
> /usr/local/freesurfer/bin/mri_nu_correct.mni
> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
> nIters 1
> $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
> Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
> Sat Mar 11 14:48:05 IST 2017
> /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
> /usr/bin/bc
> tmpdir is ./tmp.mri_nu_correct.mni.10571
> /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
> mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from orig.mgz...
> TR=483.49, TE=12.00, TI=0.00, flip angle=73.00
> i_ras = (-1, 9.77889e-09, 1.16415e-09)
> j_ras = (5.82077e-09, 0, -1)
> k_ras = (1.21945e-08, 1, 0)
> changing data type from uchar to float (noscale = 0)...
> writing to ./tmp.mri_nu_correct.mni.10571/nu0.mnc...
>
> --------------------------------------------------------
> Iteration 1 Sat Mar 11 14:48:07 IST 2017
> nu_correct -clobber ./tmp.mri_nu_correct.mni.10571/nu0.mnc ./tmp.mri_nu_correct.mni.10571/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10571/0/ -iterations 1000 -distance 50
> /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied.
> ERROR: nu_correct
> Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s testsample exited with ERRORS at Sat Mar 11 14:48:07 IST 2017
>
> freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
> Platform: Cent OS 7
>
> uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
>
> Sent from Outlook
> <recon-all.log>_______________________________________________
> Freesurfer mailing list
>
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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Message: 7
Date: Sat, 11 Mar 2017 09:23:16 -0500
From: shi yao wang <
wangshiyao2009@gmail.com>
Subject: [Freesurfer] How to check if FS are processing correctly.
To:
freesurfer@nmr.mgh.harvard.eduMessage-ID:
<
CA+rJNW8KaPQ5jyZcrTHBrP8cb8GziGzq=7z3ZrZ5xuBuL0bdvg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear FS experts:
I am using FS to analyze our MRI data.
When I finished recon -all, there are following informaion:
Started at Fri Mar 10 11:26:05 EST 2017
Ended at Fri Mar 10 18:26:51 EST 2017
#@#%# recon-all-run-time-hours 7.013
recon-all -s 10001 finished without error at Fri Mar 10 18:26:51 EST 2017
Does that mean every steps is correct? (although there were some error
message when I checking recon -all. log file).
thanks
Lawrence
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Message: 8
Date: Sat, 11 Mar 2017 10:13:36 -0500 (EST)
From: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Intensity normalization in longitudinal
processing
To: Freesurfer support list <
freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<
alpine.LRH.2.20.1703111013150.16530@door.nmr.mgh.harvard.edu>
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HI Jaiashre
is there a reason to mix versions? We always advise against this
cheers
Bruce
On Fri, 10
Mar 2017, Jaiashre Sridhar wrote:
>
> Hello FreeSurfer Team,
>
> ?
>
> For a longitudinal study, we processed the cross-sectional scans through FS
> v5.1 and ran the longitudinal stream in FS v6.0. The voxel intensities in
> wm.mgz of the long timepoints are variable and are much lower (not in the
> range of 110).
>
> ?
>
> I have attached the image of a longitudinal timepoint created in v6.0 and
> compared it to the one created in v5.1 (The cross brain recons for both of
> them were done in v5.1). The white and pial surfaces look similar across
> versions but the long created in v6.0 does not have a uniform intensity
> compared to the one created in v5.1. Should this matter as long as the
> surfaces look fine?
>
> ?
>
> I tried to use expert options with ?mri_normalize ?gentle? while creating
> the long in v6.0 but it did not help. Any suggestions to achieve a better
> intensity normalization?
>
> ?
>
> Thank you,
>
> Jaiashre.
>
> ?
>
>
>
------------------------------
Message: 9
Date: Sat, 11 Mar 2017 10:19:19 -0500 (EST)
From: Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRI intensity normalize
To: Freesurfer support list <
freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<
alpine.LRH.2.20.1703111019090.16530@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
you can, but why do you need to do it outside of the recon-all stream?
On
Fri, 10 Mar 2017, shi yao wang wrote:
> Dear FS experts,?I am wondering the process of MRI intensity normalization.?
> Before I am running recon -all, can I run following process to normalize our
> MRI images.?
>
> mri_normalize SUBJECT/mri/nu SUBJECT/mri/wm
>
> or any other preprocessing methods to avoid bias.?
>
> thanks
> Lawrence
> Emory University
>
>
------------------------------
Message: 10
Date: Sat, 11 Mar 2017 09:28:42 -0600
From: Octavian Lie <
octavian.lie@gmail.com>
Subject: [Freesurfer] -dura_thresh
To: "
freesurfer@nmr.mgh.harvard.edu" <
freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<
CACnobxQsd=E=-P7omyJLJ70fP=b9F-2ReA6FyvcpeTGH9Y-1TQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear All,
In FS6.0.0, this flag is added to manually adjust watershed threshold
instead of its automatic calculation. I went back to the original paper by
Segonne et al, and I could identify the prefllooding height h and the post
watershed threshold t. I assume the flag refers to the latter.
Since the threshold varies between subjects, where is it specified in the
log file of a recon-all run?
Also, could you indicate a (narrow) range one could start with if trying to
manually adjust a run, based on your experience? Also, what is the
watershed direction based on t (higher t values lead to more aggressive
dura removal, or the other way around?
Thank you very much,
Octavian
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