Re: [Freesurfer] Highlighting single atlas structures in freeview

2019-01-23 Thread Francesco Puccettone 
External Email - Use Caution

Hi Andrew,

Thank you very much for this, I will give this a try when I next have
access to that PC, which will unfortunately not be very soon.

Until then, since the task I set out to do is quite straighforward, I was
wondering if there is a workaround to make the old Freeview (v5.3, which I
still consider an excellent and versatile tool) to do it as well, that is,
to highlight atlas parcels one at a time.

In either case I will report back once I am able to update those libraries.

Best,
--F.

On Tue, 22 Jan 2019 at 17:16, Hoopes, Andrew 
wrote:

> Hi Francesco, the linux dev distributions are built on 64bit centos6 and
> 7, so you’re right about your original issue being related to the 32bit vm.
> I think your newer Qt errors are related to out-of-date libraries supplied
> in the ‘Update Freeview’ instructions. I’ve just updated that wiki page (at
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview) so it can
> account for changing Qt libraries. Can you give those new instructions a
> try and let me know how it goes?
>
>
>
> thanks,
>
> Andrew
>
>
>
>
>
> *From: * on behalf of Francesco
> Puccettone 
> *Reply-To: *FS Help 
> *Date: *Tuesday, January 22, 2019 at 5:40 AM
> *To: *FS Help 
> *Subject: *Re: [Freesurfer] Highlighting single atlas structures in
> freeview
>
>
>
> *External Email - Use Caution*
>
> As per an older thread
> ,
> this might be in fact due to the VM being 32bit. It is mentioned there
> the 64bit VirtualBox image is widely available, but I on the main FS
> website I can only find the 32bit 5.3 version
> 
>  for
> VirtualBox.
>
>
>
> I also have a FS 6.0 64bit installation on a Linux PC, and I tried the
> same update commands there. But there is still an error at the end when I
> try to start freeview:
>
>
>
> *freeview: relocation error: freeview: symbol
> _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent, version Qt_5 not
> defined in file libQt5Widgets.so.5 with link time reference*
>
>
>
> Thanks still..
>
> --Francesco
>
>
>
> On Tue, 22 Jan 2019 at 11:20, Francesco Puccettone <
> francesco.puccett...@gmail.com> wrote:
>
> Hi Ruopeng,
>
>
>
> Thanks! I took those steps to update Freeview, but when I try to start
> (the updated) Freeview, the command line returns "bash:
> /usr/local/freesurfer/bin/freeview: cannot execute binary file".
>
>
>
> Maybe there is something wrong in the update instructions, possibly the
> library-update command (which has the -C option) or the chmod command?
>
>
>
> I am using freesurfer-Linux-centos4-stable-pub-v5.3.0 inside an Oracle VM
> Virtualbox.
>
>
>
> --F.
>
>
>
> On Mon, 21 Jan 2019 at 19:30, Ruopeng Wang 
> wrote:
>
> HI Francesco,
>
>
>
> The latest development version of freeview can do this. You can download
> it from here:
>
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
>
>
>
> Best,
>
> Ruopeng
>
>
>
> On Jan 21, 2019, at 8:54 AM, Francesco Puccettone <
> francesco.puccett...@gmail.com> wrote:
>
>
>
> *External Email - Use Caution*
>
>
>
> Dear all,
>
>
>
> I would like to show several structures from the DKT (or the
> Desikan-Killiany) atlas alone on a "blank" fsaverage brain, rather than
> have all structures displayed in different colors (as happens by default).
> For instance, I'd like to just show "medialorbitofrontal" on its own, then
> "middletemporal" on its own, etc.
>
>
>
> After I open the parcellation,
>
> freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f
> /FS/fsaverage/surf/lh.white:annot=aparc.annot
>
> , I expected to be able to turn each label in the list on and off like a
> layer, but this does not work.
>
> <21-01-2019 14.48.54.jpg>
>
>
>
> I hoped I could use Alt+F to hide/show each atlas label at a time (cf
> freeview tutorial
> ),
> but this instead toggles the entire external surface of the brain on and
> off.
>
>
>
> Can anyone help? Thank you!
>
> --Francesco
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
>
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Re: [Freesurfer] FSFAST poor registration

2019-01-23 Thread Keri Woods 
External Email - Use Caution

Hi Douglas

Thanks for the response.

No, some of the registrations are fine. Some are close, but not perfect,
while others are very bad.

I've checked the subjectname file for some subjects with poor registration
(eg 20_101), and they are correct.

Thanks,
Keri

On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Are you saying that all of them have bad registrations? Some of them
> (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101)
> look like they could be bad. For the bad ones, are you totally sure that
> the subjetname file has the correct name of the subject?
>
> On 1/21/19 3:19 AM, Keri Woods wrote:
> >
> > External Email - Use Caution
> >
> > Hi Douglas
> >
> > Thank you for your reply.
> >
> > I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> >
> > I am using whole brain data. The functional and structural images were
> > acquired in different sessions on the same day, I don't know if that
> > complicated things? Each subject has 2 runs of the same task.
> >
> > This is what I get after running the command in the format of
> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum
> >
> > 20_1   013 0.5155
> > 20_1   014 0.5090
> > 20_10  013 0.5247
> > 20_10  014 0.5229
> > 20_100 038 0.8420
> > 20_100 040 0.8443
> > 20_101 008 0.9052
> > 20_101 010 0.9289
> > 20_102 058 0.6924
> > 20_102 059 0.6902
> > 20_103 045 0.9778
> > 20_103 046 0.9931
> > 20_104 010 0.9324
> > 20_104 012 0.9413
> > 20_105 013 0.8754
> > 20_105 014 0.8937
> > 20_106 047 0.4433
> > 20_106 048 0.4377
> > 20_107 008 0.9178
> > 20_107 010 0.9238
> > 20_11  013 0.7631
> > 20_11  014 0.7615
> > 20_110 048 0.7687
> > 20_110 049 0.7549
> > 20_112 013 0.8821
> > 20_112 014 0.9161
> > 20_113 052 0.7689
> > 20_113 053 0.7757
> > 20_116 046 1.0072
> > 20_116 047 1.0256
> > 20_117 008 0.7742
> > 20_117 010 0.7826
> > 20_119 013 0.7929
> > 20_119 014 0.7854
> > 20_120 048 0.5090
> > 20_120 049 0.4973
> > 20_126 047 0.8285
> > 20_126 048 0.8281
> > 20_128 046 0.9580
> > 20_128 047 0.9314
> > 20_130 047 0.9439
> > 20_130 048 0.9425
> > 20_132 047 0.8550
> > 20_132 048 0.8558
> > 20_134_1   013 0.5716
> > 20_134_1   015 0.5744
> > 20_135 011 0.8357
> > 20_135 012 0.8401
> > 20_136 044 0.9995
> > 20_136 045 0.9604
> > 20_137 047 0.7922
> > 20_137 048 0.7990
> > 20_142 047 0.5282
> > 20_142 048 0.5278
> > 20_144 013 0.8755
> > 20_144 014 0.8838
> > 20_146 047 0.7997
> > 20_146 048 0.7895
> > 20_149 049 0.9251
> > 20_149 050 0.9408
> > 20_151 048 0.5905
> > 20_151 049 0.5519
> > 20_152 048 0.9024
> > 20_152 049 0.9021
> > 20_155 048 0.5285
> > 20_155 049 0.5324
> > 20_156 048 0.8883
> > 20_156 049 0.9267
> > 20_158 048 0.5404
> > 20_158 049 0.5297
> > 20_159 048 0.8021
> > 20_160 013 0.5002
> > 20_160 014 0.4942
> > 20_162 047 0.5401
> > 20_162 048 0.5401
> > 20_164 047 0.8944
> > 20_164 048 0.8940
> > 20_165 047 0.9163
> > 20_165 048 0.9077
> > 20_166 045 0.8787
> > 20_166 046 0.8848
> > 20_167 050 0.8428
> > 20_167 051 0.8442
> > 20_169 049 0.9407
> > 20_169 050 0.9462
> > 20_170 047 0.8921
> > 20_170 048 0.9113
> > 20_171 013 0.9060
> > 20_171 014 0.9060
> > 20_173 048 0.9193
> > 20_173 049 0.9141
> > 20_177 048 0.8695
> > 20_177 049 0.8600
> > 20_178 048 1.0327
> > 20_178 049 0.8979
> > 20_180 045 0.7999
> > 20_180 046 0.8002
> > 20_182 047 0.9135
> > 20_182 048 0.9130
> > 20_184 048 0.9842
> > 20_184 049 0.9960
> > 20_185 046 0.9640
> > 20_185 047 0.9514
> > 20_187 048 0.8134
> > 20_187 049 0.8082
> > 20_189 047 1.0063
> > 20_189 048 0.9701
> > 20_19  013 0.8485
> > 20_19  014 0.8534
> > 20_190 047 0.9279
> > 20_190 048 0.9169
> > 20_191 046 0.9586
> > 20_191 047 0.9751
> > 20_192 049 0.8544
> > 20_193 013 0.9084
> > 20_193 014 0.9110
> > 20_194 047 0.9220
> > 20_194 048 0.9166
> > 20_195 048 0.9552
> > 20_195 049 0.9508
> > 20_196 047 0.9098
> > 20_196 048 0.9011
> > 20_199 048 0.8569
> > 20_199 049 0.8567
> > 20_20  013 0.8750
> > 20_20  014 0.8749
> > 20_201 048 0.8864
> > 20_201 049 1.0040
> > 20_202 048 0.8542
> > 20_202 049 0.8516
> > 20_203 048 1.0267
> > 20_203 049 1.0060
> > 20_204 048 0.8513
> > 20_204 049 0.8588
> > 20_208 014 0.9130
> > 20_208 015 0.9329
> > 20_209 047 1.0020
> > 20_209 048 1.0120
> > 20_21  027 0.9747
> > 20_21  028 1.0081
> > 20_210 048 0.8607
> > 20_210 049 0.8564
> > 20_220 047 0.
> > 20_220 048

[Freesurfer] Double cursors when viewing inflated surfaces

2019-01-23 Thread Bunting, Emma 
External Email - Use Caution

Hi, 

When I load my surface overlay (sig.mgh output file from GLM analysis) onto fs 
average lh inflated surface, I see two cursors when looking at the inner side 
of the brain. When i click the outer side, only one cursor shows. 

I have used this command to visualise the data: freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:anot_outline=1:overlay=glmdir/matrix/sig.mgh:overlay_threshold=4,5
 -viewport 3d

I’ve worried that the labels its loading onto the brain aren'’t aligning 
properly if the cursor is in 2 places. 

Is there something wrong with my data visualisation command?

Thanks in advance, 

Best wishes, 

Emma 

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Re: [Freesurfer] FSFAST poor registration

2019-01-23 Thread Keri Woods 
External Email - Use Caution

I meant some are nearly perfect.

On Wed, Jan 23, 2019 at 11:49 AM Keri Woods  wrote:

> Hi Douglas
>
> Thanks for the response.
>
> No, some of the registrations are fine. Some are close, but not perfect,
> while others are very bad.
>
> I've checked the subjectname file for some subjects with poor registration
> (eg 20_101), and they are correct.
>
> Thanks,
> Keri
>
> On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Are you saying that all of them have bad registrations? Some of them
>> (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101)
>> look like they could be bad. For the bad ones, are you totally sure that
>> the subjetname file has the correct name of the subject?
>>
>> On 1/21/19 3:19 AM, Keri Woods wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Douglas
>> >
>> > Thank you for your reply.
>> >
>> > I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>> >
>> > I am using whole brain data. The functional and structural images were
>> > acquired in different sessions on the same day, I don't know if that
>> > complicated things? Each subject has 2 runs of the same task.
>> >
>> > This is what I get after running the command in the format of
>> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run
>> -bbr-sum
>> >
>> > 20_1   013 0.5155
>> > 20_1   014 0.5090
>> > 20_10  013 0.5247
>> > 20_10  014 0.5229
>> > 20_100 038 0.8420
>> > 20_100 040 0.8443
>> > 20_101 008 0.9052
>> > 20_101 010 0.9289
>> > 20_102 058 0.6924
>> > 20_102 059 0.6902
>> > 20_103 045 0.9778
>> > 20_103 046 0.9931
>> > 20_104 010 0.9324
>> > 20_104 012 0.9413
>> > 20_105 013 0.8754
>> > 20_105 014 0.8937
>> > 20_106 047 0.4433
>> > 20_106 048 0.4377
>> > 20_107 008 0.9178
>> > 20_107 010 0.9238
>> > 20_11  013 0.7631
>> > 20_11  014 0.7615
>> > 20_110 048 0.7687
>> > 20_110 049 0.7549
>> > 20_112 013 0.8821
>> > 20_112 014 0.9161
>> > 20_113 052 0.7689
>> > 20_113 053 0.7757
>> > 20_116 046 1.0072
>> > 20_116 047 1.0256
>> > 20_117 008 0.7742
>> > 20_117 010 0.7826
>> > 20_119 013 0.7929
>> > 20_119 014 0.7854
>> > 20_120 048 0.5090
>> > 20_120 049 0.4973
>> > 20_126 047 0.8285
>> > 20_126 048 0.8281
>> > 20_128 046 0.9580
>> > 20_128 047 0.9314
>> > 20_130 047 0.9439
>> > 20_130 048 0.9425
>> > 20_132 047 0.8550
>> > 20_132 048 0.8558
>> > 20_134_1   013 0.5716
>> > 20_134_1   015 0.5744
>> > 20_135 011 0.8357
>> > 20_135 012 0.8401
>> > 20_136 044 0.9995
>> > 20_136 045 0.9604
>> > 20_137 047 0.7922
>> > 20_137 048 0.7990
>> > 20_142 047 0.5282
>> > 20_142 048 0.5278
>> > 20_144 013 0.8755
>> > 20_144 014 0.8838
>> > 20_146 047 0.7997
>> > 20_146 048 0.7895
>> > 20_149 049 0.9251
>> > 20_149 050 0.9408
>> > 20_151 048 0.5905
>> > 20_151 049 0.5519
>> > 20_152 048 0.9024
>> > 20_152 049 0.9021
>> > 20_155 048 0.5285
>> > 20_155 049 0.5324
>> > 20_156 048 0.8883
>> > 20_156 049 0.9267
>> > 20_158 048 0.5404
>> > 20_158 049 0.5297
>> > 20_159 048 0.8021
>> > 20_160 013 0.5002
>> > 20_160 014 0.4942
>> > 20_162 047 0.5401
>> > 20_162 048 0.5401
>> > 20_164 047 0.8944
>> > 20_164 048 0.8940
>> > 20_165 047 0.9163
>> > 20_165 048 0.9077
>> > 20_166 045 0.8787
>> > 20_166 046 0.8848
>> > 20_167 050 0.8428
>> > 20_167 051 0.8442
>> > 20_169 049 0.9407
>> > 20_169 050 0.9462
>> > 20_170 047 0.8921
>> > 20_170 048 0.9113
>> > 20_171 013 0.9060
>> > 20_171 014 0.9060
>> > 20_173 048 0.9193
>> > 20_173 049 0.9141
>> > 20_177 048 0.8695
>> > 20_177 049 0.8600
>> > 20_178 048 1.0327
>> > 20_178 049 0.8979
>> > 20_180 045 0.7999
>> > 20_180 046 0.8002
>> > 20_182 047 0.9135
>> > 20_182 048 0.9130
>> > 20_184 048 0.9842
>> > 20_184 049 0.9960
>> > 20_185 046 0.9640
>> > 20_185 047 0.9514
>> > 20_187 048 0.8134
>> > 20_187 049 0.8082
>> > 20_189 047 1.0063
>> > 20_189 048 0.9701
>> > 20_19  013 0.8485
>> > 20_19  014 0.8534
>> > 20_190 047 0.9279
>> > 20_190 048 0.9169
>> > 20_191 046 0.9586
>> > 20_191 047 0.9751
>> > 20_192 049 0.8544
>> > 20_193 013 0.9084
>> > 20_193 014 0.9110
>> > 20_194 047 0.9220
>> > 20_194 048 0.9166
>> > 20_195 048 0.9552
>> > 20_195 049 0.9508
>> > 20_196 047 0.9098
>> > 20_196 048 0.9011
>> > 20_199 048 0.8569
>> > 20_199 049 0.8567
>> > 20_20  013 0.8750
>> > 20_20  014 0.8749
>> > 20_201 048 0.8864
>> > 20_201 049 1.0040
>> > 20_202 048 0.8542
>> > 20_202 049 0.8516
>> > 20_203 048 1.0267
>> > 20_203 049 1.0060
>> > 20_204 048 0.8513
>> > 20_

[Freesurfer] correction for multiple comparison: simulation vs grf vs cache

2019-01-23 Thread john Anderson 
External Email - Use Caution

Hi Dr Greve,
I would like to correct surface based analyses of PET data for multiple 
comparisons. I ran group comparisons in three spaces. left and right 
hemispheres and subcortical.
I used the method --cache in mri_glmfit-sim to correct the analyses in eft and 
right hemispheres.
I used the method --grf in mri_glmfit-sim to correct the analyses in 
subcortical regions.
My questions are:

In one of your kind responses to a collegue here 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-January/035650.html
you had suggested  "If you want to use GRF, you should use smooth by twice the 
native voxel size. I would not go higher than .01 on the threshold".
Would you mind clarify what it means don;t go higher than .01 is this the cwp 
threshold? also smoothing by twice the native voxel is this means fwhm=2mm?

The methods --cache and --grf are giving me the expected results.. when  I 
should consider using simulation --perm ?

Thanks for any clarification
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Re: [Freesurfer] Highlighting single atlas structures in freeview

2019-01-23 Thread Francesco Puccettone 
External Email - Use Caution

PS: I guess this is possible in older versions as well based on figures in
older papers (such as Fig 1 in this

one), that show certain ROIs on a blank fsaverage, just as I aim to do now.
--F.

On Wed, 23 Jan 2019 at 10:06, Francesco Puccettone <
francesco.puccett...@gmail.com> wrote:

> Hi Andrew,
>
> Thank you very much for this, I will give this a try when I next have
> access to that PC, which will unfortunately not be very soon.
>
> Until then, since the task I set out to do is quite straighforward, I was
> wondering if there is a workaround to make the old Freeview (v5.3, which I
> still consider an excellent and versatile tool) to do it as well, that is,
> to highlight atlas parcels one at a time.
>
> In either case I will report back once I am able to update those libraries.
>
> Best,
> --F.
>
> On Tue, 22 Jan 2019 at 17:16, Hoopes, Andrew 
> wrote:
>
>> Hi Francesco, the linux dev distributions are built on 64bit centos6 and
>> 7, so you’re right about your original issue being related to the 32bit vm.
>> I think your newer Qt errors are related to out-of-date libraries supplied
>> in the ‘Update Freeview’ instructions. I’ve just updated that wiki page (at
>> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview) so it can
>> account for changing Qt libraries. Can you give those new instructions a
>> try and let me know how it goes?
>>
>>
>>
>> thanks,
>>
>> Andrew
>>
>>
>>
>>
>>
>> *From: * on behalf of Francesco
>> Puccettone 
>> *Reply-To: *FS Help 
>> *Date: *Tuesday, January 22, 2019 at 5:40 AM
>> *To: *FS Help 
>> *Subject: *Re: [Freesurfer] Highlighting single atlas structures in
>> freeview
>>
>>
>>
>> *External Email - Use Caution*
>>
>> As per an older thread
>> ,
>> this might be in fact due to the VM being 32bit. It is mentioned there
>> the 64bit VirtualBox image is widely available, but I on the main FS
>> website I can only find the 32bit 5.3 version
>> 
>>  for
>> VirtualBox.
>>
>>
>>
>> I also have a FS 6.0 64bit installation on a Linux PC, and I tried the
>> same update commands there. But there is still an error at the end when I
>> try to start freeview:
>>
>>
>>
>> *freeview: relocation error: freeview: symbol
>> _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent, version Qt_5 not
>> defined in file libQt5Widgets.so.5 with link time reference*
>>
>>
>>
>> Thanks still..
>>
>> --Francesco
>>
>>
>>
>> On Tue, 22 Jan 2019 at 11:20, Francesco Puccettone <
>> francesco.puccett...@gmail.com> wrote:
>>
>> Hi Ruopeng,
>>
>>
>>
>> Thanks! I took those steps to update Freeview, but when I try to start
>> (the updated) Freeview, the command line returns "bash:
>> /usr/local/freesurfer/bin/freeview: cannot execute binary file".
>>
>>
>>
>> Maybe there is something wrong in the update instructions, possibly the
>> library-update command (which has the -C option) or the chmod command?
>>
>>
>>
>> I am using freesurfer-Linux-centos4-stable-pub-v5.3.0 inside an Oracle VM
>> Virtualbox.
>>
>>
>>
>> --F.
>>
>>
>>
>> On Mon, 21 Jan 2019 at 19:30, Ruopeng Wang 
>> wrote:
>>
>> HI Francesco,
>>
>>
>>
>> The latest development version of freeview can do this. You can download
>> it from here:
>>
>>
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
>>
>>
>>
>> Best,
>>
>> Ruopeng
>>
>>
>>
>> On Jan 21, 2019, at 8:54 AM, Francesco Puccettone <
>> francesco.puccett...@gmail.com> wrote:
>>
>>
>>
>> *External Email - Use Caution*
>>
>>
>>
>> Dear all,
>>
>>
>>
>> I would like to show several structures from the DKT (or the
>> Desikan-Killiany) atlas alone on a "blank" fsaverage brain, rather than
>> have all structures displayed in different colors (as happens by default).
>> For instance, I'd like to just show "medialorbitofrontal" on its own, then
>> "middletemporal" on its own, etc.
>>
>>
>>
>> After I open the parcellation,
>>
>> freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f
>> /FS/fsaverage/surf/lh.white:annot=aparc.annot
>>
>> , I expected to be able to turn each label in the list on and off like a
>> layer, but this does not work.
>>
>> <21-01-2019 14.48.54.jpg>
>>
>>
>>
>> I hoped I could use Alt+F to hide/show each atlas label at a time (cf
>> freeview tutorial
>> ),
>> but this instead toggles the entire external surface of the brain on and
>> off.
>>
>>
>>
>> Can anyone help? Thank you!
>>
>> --Francesco
>>
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>>
>>
>>
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>>

[Freesurfer] move statistical map onto the cerebellum surface

2019-01-23 Thread john Anderson 
External Email - Use Caution

Dear FS experts,
I ran surface based PET analysis on subcortical regions. Then corrected the 
results for multiple comparisons using  the method --grf in the command 
mri_glmfit-sim.

I can visualize the output of multiple comparisons (i.e. the file 
grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this statistical map 
shows difference between the groups in the cerebellum Instead of 
visualizing the results on volume, I want to move this file to the cerebellum 
surface. I already created the cerebellum surfaces from aseg.mgz file in 
fsaverage using the command mris_tesselate.

How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume space and 
map it on the cerebellum surface?

I tried mri_vol2surf but this command requires the flag --hemi as a result it 
will map the file "grf.th1.3.pos.sig.cluster.mgh" on cerebral hemispheres (lh 
or rh) but not the cerebellum..
How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the cerebellum 
surface?

Thanks for any suggestions,
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[Freesurfer] Functional connectivty walkthrough step 8 error

2019-01-23 Thread Amrita Bedi 
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Hi Dr Greve,

Attached is the log file.

On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Can you send the full terminal output and/or the log file?
>
> On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer developers,
> >
> > I was following the functional connectivity walkthrough for resting
> > stage BOLD data and I got the attached error when I ran step 8
> > (selxavg3-sess). Does anyone have any thoughts on how to trouble shoot
> > this?
> > Not sure if it’s of any use but I ran this using Freesurfer 6.0 on
> > Centos 7.4
> >
> > Thank You.
> >
> > Best
> > Amrita
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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selxavg3-sess-Bold1-fc.lpccseed.surf.lh-190122151015.log
Description: Binary data
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Re: [Freesurfer] "slides" link is not working

2019-01-23 Thread Greve, Douglas N.,Ph.D. 
try this one
http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx


On 1/22/19 7:47 PM, Peters, Douglas G wrote:
>
> External Email - Use Caution
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
>
>
> Error Message:
>
>
>   Not Found
>
> The requested URL /pub/docs/freesurfer.groupanalysis.short.pdf was not 
> found on this server.
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

2019-01-23 Thread Daniel Leopold 
External Email - Use Caution

Hello FS experts and enthusiasts,

Thus far, I have used mri_concat to make 4D files of subjects'
lh.thickness.fwhm15.fsaverage.mgh files to be used as input for palm. The
results maps are of the .mgz format. I can convert these to .nii using
mri_convert in order to use fslmaths or fslstats. My dilemma is that I'd
like to use another viewing package for the palm results (i.e., Surf Ice)
because of its features and some quirks I've encountered while loading
results in Freeview. Surf Ice accepts a number of formats (
https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_Formats),
including Freesurfer's .asc, .srf, .curv, .gcs, .pial, and .w (among
*many* others),
but I have yet to successfully convert these .mgz maps to a readable
format. Surf Ice can read .nii, but loading my mri_converted .nii files
results in a uniform surface with 0 at all vertices. Thus, I have two
questions:

1) Can you think of a means to convert these surface "volumes" (.mgh/.mgz)
to a desired format that can be read by Surf Ice? I've attempted
mri_vol2surf, mri_surf2surf, and mris_convert, but cannot find an
appropriate format/get things to work.
In case it's helpful, readable formats are:

2) My alternative idea would be to instead use mri_concat on subjects'
lh.thickness files and later apply fwhm smoothing. Would this approach be
feasible? I could test whether pre-palm smoothed and post-palm smoothed
results are equivalent, but I'm afraid that the variable dimensions of
subjects' native thickness files would cause problems either with palm or
when later trying to view the group-level results.

Version information:
Recon-all run with FreeSurfer 5.3.0
FSL 5.0.8
palm alpha112

Thank you in advance for any suggestions, and please let me know if any
additional information would be helpful.


With gratitude,
Dan
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