Re: [Freesurfer] correlation analysis two groups (paired analysis)

[Agurne Sampedro Calvete]

External Email - Use Caution

Thank you very much for your rapid response.
Best regards,




*-- --*

*Agurne Sampedro Calvete, PhD*




Departamento de Psicología / Psikologia Saila / Department of Psychology
Facultad de Ciencias de la Salud / Osasun Zientzien Fakultatea / Faculty of
Health Sciences
Neuropsychology of Severe Medical Conditions Research Team - Neurolab
http://secure-web.cisco.com/1gsFGeZNf08M2NUekGr8282Ehtf620Mb3MaIqgn4S6h30847r7oUoGC9FK00VgiwjZsZZZmQbjGYYXiM45sK40WjqLTCgkCAWl12J6Dl7CAAyhcFS_u8zwSpmAWFvg3XHakNiKkcL2inCOrNAsOow4dm13cHT8uEAaF0ibBqgTyvlt8EVdZJ81oxKtr89zmd7GFLPflGXMYhnb-iPuNc64gN8ESKXNOuZ1UhSjctYFTJdhqGz35D7g09fUD1zOxQG7YNRBT7cTHtkGyGoJH8FWsUKo_nAUJDMHK2pGaXXHL14EtGo8e8ui-ugS7ejO6qcLgjA62GU6ms3ft5Nhsnuww/http%3A%2F%2Fwww.neurolab.deusto.es


Universidad de Deusto / Deustuko Unibertsitatea/ University of Deusto
Avda de las Universidades 24, 48007, Bilbao (Spain)
Phone: +34 94 413 90 00 (ext 3015)
Office:  
https://secure-web.cisco.com/1V1rBfZ8JjCamegLyFj5UeLkH2vv3nZmVOnRrIltvzrumikTnZq5wlfxGXxO0tfdARR68MrvXvz1IwXCHukhtwrevIaEkPafARoAKklKzHZ8d4D_l5FET9yICENlyy5QGWjZC-mFF6Un4Q2Nm2gU2IBp9lbVNmI4ODyWwggZNYxmjhxEPDDKxXEPUwLSnE-aXuzp74er1_eyGF3-Ru_l9-U2mOk7vwt_DKc6Tgj-ddBmrMQ4NF_oEvg5TJ5wu9Kaxvtm9xYp3Qt_jvjzn5ZrbfWEx4vE_mYyWtddpj1AXg9tb-RILduMKWvvgLK2rEyNGxD2wxc7efBO6WTaH7sWhSw/https%3A%2F%2F360bio.deusto.es%2FG1Sd6OTDmx%2F7787023p%2646.06h%26125.76t




El jue, 12 ene 2023 a las 15:47, Douglas N. Greve ()
escribió:

> If you are looking for the difference in the correlation between the
> groups then you have to use DODS and 0 0 1 -1. The way to understand it is
> that you have four regression coefficients and each means something. The
> way you have it set up in the fsgd file is that they are
> 1. group 1 intercept
> 2. group 2 intercept
> 3. group 1 cognition slope
> 4. group 2 coginition slope
> Each coefficient gets multipled by its corresponding weight in the
> contrast and then the results are summed. So if you use 0 0 1 -1 you end up
> with contrast = g1cogslope-g2cogslope which is the difference you want
>
> If you are just interested in whether the cog slope changes without regard
> to the group, then you would use 0 0 0.5 0.5 which means contrast =
> 0.5*g1cogslope + 0.5*g2cogslope which is the average of the slopes. In this
> case, using DOSS and 0 0 1 will give you the same results if there is no
> difference in the cog slopes between the groups
>
>
>
> On 1/12/2023 8:48 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear FreeSurfer experts,
>
> I have two groups and two time points and I would like to do a correlation
> analysis between a variable (cognition) and the change score in cortical
> thickness between the two time points (time2 minus time1).
>
> I would like to see if the *correlation *is *different *among each group,
> if there is an interaction with the group.
>
> I have followed the paired t test instructions (*MailScanner has detected
> a possible fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1fXRzP-yKkgu2fox62nZ66JPTjq0Td7zmK1ZioRYjE3sOtWBVcRad5qQ2gNkUmrOUFGnSEa_KqBRd4DzzAdkpmsbtFMP3K9W2eUQ_RZY06JLsRN2e2JwfGuJJp9ndeYQ6-UZAGLUOY1qvHqzvldBbNtFotUoSWnIe15P2ZeSmtTuR0eFJqXO9Y2iiEgk9qzkBvEXqE90dhempmajzakTeA3OdF7Cyu7QJ7-AGj8fy__f4HsLaodXcsF9ObktBlZMQeyRV0H-iAltyQCG5cLqTOO18sPEwkvrzlgezAizxryjnbXLSQi7q1UgJeSINzyXK2D5pLsukLD7yUXs1olLpcg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
> <https://secure-web.cisco.com/11YHUupGYyGBe5w6QAQb3OOLcNluK0Tqv4VUmAmDx5wuogvWlaypoD3OpvEWBM2c4Wa29T38k5k4_bq_JXA-kc8P0mACbCulAMmVSDKvC4Tl7x6Gk2A_azFExScL0y5HFngabH5bZRoIDy_dKvAtXkXegvTr-2ftNMkD3TQlTwaQtCSI-0554BriqrUu1MKXy2ZDf8l6cSP5im59p93FqJma0yYa3cYXujDp-aXCIOKlUXzojlgBIskwrWMiPG0pmIn08tOj1OYgSExrdJrOrWu2iAIGdhvSK3iuWEQ7BCEp4De-DPfIldNoZfbygVQ1mrt9CvPacDWwenDkjC7Q40A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis>),
> but I am not sure about the contrast(s) I have to use.
>
> The paired-diff.fsgd file (second fsgd file) is the following:
>
> GroupDescriptorFile 1
> Title OSGM
> Class Group1
> Class Group2
> Variables cognition
> Input subject1pair Group1 0.546
> Input subject1pair Group2 -0.243
> ...
>
> How should it be the contrasts files to see the *correlation *of the
> variable cognition with the change score in thickness taking into account
> the groups? And should I use DODS or DOSS?
>
> Using DODS:
> 0 0 0.5 0.5
>  or
> 0 0 1 -1
>
> I don't understand the difference between both contrasts. I think I should
> use the one of "0 0 1 -1" to see whether the cognition variable correlates
> with change in thickness differently according to the group. Is this
> correct?
>
> Using DOSS:
> 0 0 1
>
> Thank you very

[Freesurfer] correlation analysis two groups (paired analysis)

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear FreeSurfer experts,

I have two groups and two time points and I would like to do a correlation
analysis between a variable (cognition) and the change score in cortical
thickness between the two time points (time2 minus time1).

I would like to see if the *correlation *is *different *among each group,
if there is an interaction with the group.

I have followed the paired t test instructions (
https://secure-web.cisco.com/11YHUupGYyGBe5w6QAQb3OOLcNluK0Tqv4VUmAmDx5wuogvWlaypoD3OpvEWBM2c4Wa29T38k5k4_bq_JXA-kc8P0mACbCulAMmVSDKvC4Tl7x6Gk2A_azFExScL0y5HFngabH5bZRoIDy_dKvAtXkXegvTr-2ftNMkD3TQlTwaQtCSI-0554BriqrUu1MKXy2ZDf8l6cSP5im59p93FqJma0yYa3cYXujDp-aXCIOKlUXzojlgBIskwrWMiPG0pmIn08tOj1OYgSExrdJrOrWu2iAIGdhvSK3iuWEQ7BCEp4De-DPfIldNoZfbygVQ1mrt9CvPacDWwenDkjC7Q40A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis),
 but I am not
sure about the contrast(s) I have to use.

The paired-diff.fsgd file (second fsgd file) is the following:

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables cognition
Input subject1pair Group1 0.546
Input subject1pair Group2 -0.243
...

How should it be the contrasts files to see the *correlation *of the
variable cognition with the change score in thickness taking into account
the groups? And should I use DODS or DOSS?

Using DODS:
0 0 0.5 0.5
 or
0 0 1 -1

I don't understand the difference between both contrasts. I think I should
use the one of "0 0 1 -1" to see whether the cognition variable correlates
with change in thickness differently according to the group. Is this
correct?

Using DOSS:
0 0 1

Thank you very much in advance.

Kind regards,

Agurne
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] average thickness lobe stats

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer experts,

I am trying to obtain the average thickness of the brain lobes. I am
particularly interested in the temporal lobe.
I have run "mri_annotation2label" (--lobeStrict) and
"mris_anatomical_stats" commands and I have obtained the average thickness
of the different lobes in each hemisphere. However, I am interested in
obtaining data of both hemispheres together, that is, a single thickness
average for example for the temporal lobe. Is there a way to calculate it?
Could I just sum both averages from each hemisphere?

Thank you very much in advance.

Kind regards,

Agurne
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] longitudinal group analysis displaying results

[Agurne Sampedro Calvete]

External Email - Use Caution

Thank you very much Douglas.

Kind regards,

Agurne



Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El lun, 1 mar 2021 a las 16:52, Douglas N. Greve ()
escribió:

>
>
> On 2/26/2021 9:41 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> And is there a recommended way to compute a z value from the cluster
> p-value?
>
> You can use a p-to-z conversion; I'/m not sure it means much though
>
> With voxel-wise measure of z value, do you mean a z value of a particular
> voxel, for instance, the voxel with the maximum p value in a cluster?
>
> It could be that or the average. I don't know what you are trying to do
> here so I can't be much help
>
>
> Thank you very much.
>
> Regards,
>
> Agurne
>
>
>
>
>
> El vie, 26 feb 2021 a las 14:38, Douglas N. Greve ()
> escribió:
>
>> There is no z value for the cluster itself, but you could take the
>> cluster p-value and use it to compute a z value. Or do you want a
>> voxel-wise measure of z value?
>>
>> On 2/24/2021 4:00 AM, Agurne Sampedro Calvete wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer experts,
>>
>>  In relation to the previous question, could I obtain a Z value of the
>> significant cluster obtained by opening in freeview the z.mgh and place the
>> cursor on the point with the highest value? Is there another way to obtain
>> a Z value or alternatively, a t-value?
>>
>> Thank you very much in advance,
>>
>> Best regards,
>>
>> Agurne
>>
>> El mar, 23 feb 2021 a las 13:25, Agurne Sampedro Calvete (<
>> a.sampe...@deusto.es>) escribió:
>>
>>> Dear Freesurfer experts,
>>>
>>> I am doing a longitudinal repeated measures analysis and after
>>> correcting for multiple comparisons with Z Monte Carlo simulation (with the
>>> "mri_glmfit-sim ... --cache 3 ..." command), I obtained a significant
>>> cluster for my experimental group (pre-post).
>>>
>>> In order to obtain the information for displaying the results in the
>>> paper, I am looking at the cluster summary table. I have seen that some
>>> papers include the t value in addition to the p value, cluster size and
>>> coordinates, but how can I obtain the t value? Does it appear in the
>>> cluster summary table or elsewhere?
>>>
>>> Thank you very much in advance,
>>>
>>> Kind regards,
>>>
>>> Agurne
>>>
>>>
>>>
>>>
>>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1awj2k_ILPv2pPYn5uzF1coR--LwL2IcYiyQQt4EegX6i0hLeyYPMklwFcRkOvdSWAg_mNGIcd3dqCme9TztpK8aNd5aFJAqdajQ2u9oEOu-tgSHJaOtWm_-HzLV1Na9sAJIFaCr0J2p-NhnRoSbMIN3m71T_ZTeORMojYXvuh0OhdFqAugzictjd2jrkBr5r4jz97MV86egF-4gUbRj-SP6b-BmXlfdVYTl0wVtxDefqgcqRMMdKq2WabNbCyXlt1-kj34VVZmrhefa-hqjn3w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> <https://secure-web.cisco.com/1OuUm2ZZmU_Mv_OD-lC0xYt9uu9HkbvfOlGsBXoycxv88zfznNxK2gkZ3-BpXQHXRj5I9phInFLVPieluUvviyAJAwbB14IKeZlkCyCjLB3FPwI_ABqIWdKX5mUCCxIbrtmaXCnENNvS3zA9pFt0c3v-zkkQS-exDvqmf9shILKnHuRFXGWKAfEqZtcNirdDw3aNPjyiwrIZnOK1tR27J_UwhA1NnFDg_asS9Zeh3aE-HaumF4H2Y5bbPfmbaITYIz3-g2wGnWBQDTf7JfbkQUw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1awj2k_ILPv2pPYn5uzF1coR--LwL2IcYiyQQt4EegX6i0hLeyYPMklwFcRkOvdSWAg_mNGIcd3dqCme9TztpK8aNd5aFJAqdajQ2u9oEOu-tgSHJaOtWm_-HzLV1Na9sAJIFaCr0J2p-NhnRoSbMIN3m71T_ZTeORMojYXvuh0OhdFqAugzictjd2jrkBr5r4jz97MV86egF-4gUbRj-SP6b-BmXlfdVYTl0wVtxDefqgcqRMMdKq2WabNbCyXlt1-kj34VVZmrhefa-hqjn3w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1OuUm2ZZmU_Mv_OD-lC0xYt9uu9HkbvfOlGsBXoycxv88zfznNxK2gkZ3-BpXQHXRj5I9phInFLVPieluUvviyAJAwbB14IKeZlkCyCjLB3

Re: [Freesurfer] longitudinal group analysis displaying results

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,

And is there a recommended way to compute a z value from the cluster
p-value?
With voxel-wise measure of z value, do you mean a z value of a particular
voxel, for instance, the voxel with the maximum p value in a cluster?

Thank you very much.

Regards,

Agurne





El vie, 26 feb 2021 a las 14:38, Douglas N. Greve ()
escribió:

> There is no z value for the cluster itself, but you could take the cluster
> p-value and use it to compute a z value. Or do you want a voxel-wise
> measure of z value?
>
> On 2/24/2021 4:00 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
>  In relation to the previous question, could I obtain a Z value of the
> significant cluster obtained by opening in freeview the z.mgh and place the
> cursor on the point with the highest value? Is there another way to obtain
> a Z value or alternatively, a t-value?
>
> Thank you very much in advance,
>
> Best regards,
>
> Agurne
>
> El mar, 23 feb 2021 a las 13:25, Agurne Sampedro Calvete (<
> a.sampe...@deusto.es>) escribió:
>
>> Dear Freesurfer experts,
>>
>> I am doing a longitudinal repeated measures analysis and after correcting
>> for multiple comparisons with Z Monte Carlo simulation (with the 
>> "mri_glmfit-sim
>> ... --cache 3 ..." command), I obtained a significant cluster for my
>> experimental group (pre-post).
>>
>> In order to obtain the information for displaying the results in the
>> paper, I am looking at the cluster summary table. I have seen that some
>> papers include the t value in addition to the p value, cluster size and
>> coordinates, but how can I obtain the t value? Does it appear in the
>> cluster summary table or elsewhere?
>>
>> Thank you very much in advance,
>>
>> Kind regards,
>>
>> Agurne
>>
>>
>>
>>
>>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1OuUm2ZZmU_Mv_OD-lC0xYt9uu9HkbvfOlGsBXoycxv88zfznNxK2gkZ3-BpXQHXRj5I9phInFLVPieluUvviyAJAwbB14IKeZlkCyCjLB3FPwI_ABqIWdKX5mUCCxIbrtmaXCnENNvS3zA9pFt0c3v-zkkQS-exDvqmf9shILKnHuRFXGWKAfEqZtcNirdDw3aNPjyiwrIZnOK1tR27J_UwhA1NnFDg_asS9Zeh3aE-HaumF4H2Y5bbPfmbaITYIz3-g2wGnWBQDTf7JfbkQUw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] longitudinal group analysis displaying results

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer experts,

 In relation to the previous question, could I obtain a Z value of the
significant cluster obtained by opening in freeview the z.mgh and place the
cursor on the point with the highest value? Is there another way to obtain
a Z value or alternatively, a t-value?

Thank you very much in advance,

Best regards,

Agurne

El mar, 23 feb 2021 a las 13:25, Agurne Sampedro Calvete (<
a.sampe...@deusto.es>) escribió:

> Dear Freesurfer experts,
>
> I am doing a longitudinal repeated measures analysis and after correcting
> for multiple comparisons with Z Monte Carlo simulation (with the 
> "mri_glmfit-sim
> ... --cache 3 ..." command), I obtained a significant cluster for my
> experimental group (pre-post).
>
> In order to obtain the information for displaying the results in the
> paper, I am looking at the cluster summary table. I have seen that some
> papers include the t value in addition to the p value, cluster size and
> coordinates, but how can I obtain the t value? Does it appear in the
> cluster summary table or elsewhere?
>
> Thank you very much in advance,
>
> Kind regards,
>
> Agurne
>
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] multiple comparisons correction

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,

And can I include abs to the --grf 3 command?  I read this in the tutorial:
"NOTE: the "abs" for GRF is only approximate. For volumes, it may give very
conservative results"
Is it better to include neg or pos?
Thank you!
Regards,

Agurne

El vie, 19 feb 2021 a las 16:29, Douglas N. Greve ()
escribió:

> You have to use --grf. I never computed the cache tables for volumes
>
> On 2/19/2021 9:58 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> I have another question regarding multiple comparisons correction:
>
> Can I use --cache  with volume analyses? Or should I use --grf?
>
>
> Thank you very much,
>
> Kind regards,
>
>
> Agurne
>
>
> El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (<
> a.sampe...@deusto.es>) escribió:
>
>> Dear Douglas,
>> Thank you very much ! This paper is very helpful.
>> Regards,
>>
>> Agurne
>>
>>
>>
>>
>>
>> Neuropsychology of Severe Medical Conditions Research Team
>>
>> Dpt of Methods and Experimental Psychology
>> Faculty of Psychology and Education
>>
>> University of Deusto
>>
>> neurolab.deusto.es
>> <http://secure-web.cisco.com/1gAJEBCib9EW_ylULEVTDxDzASq_VMOoRAEIWgk_u4ErJ721bCC2wiEnNjrODzdkLXlIUmUsYnhRRjqDLlF1-Bcqys-mlDb_B2aTcm6ye1Dz08XxAm-e9QCfnFqpX3YHhkIc2TwFKsIgxRQHJTeEGrtW6m1ChKXBspuFtzKRQDbCSxIQwo8tPHgJQdt9teXZw8JgsVDegLEiWNU5Irfgx1a21XBWZK-Milh5gONHp111_8KEVyVoe2qdUfPqrPAclArlqk37HtX-_zSCMbxRkHQ/http%3A%2F%2Fneurolab.deusto.es%2F>
>>
>>
>>
>> Avda. de las Universidades 24,
>>
>> 48007, Bilbao (Spain)
>>
>> Phone: +34 944139000 (ext. 3015)
>>
>>
>> El mar, 9 feb 2021 a las 17:55, Douglas N. Greve ()
>> escribió:
>>
>>> Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1
>>> of this paper
>>>
>>> False positive rates in surface-based anatomical analysis
>>> Douglas N. Greve a, b, * , Bruce Fischl a, b
>>>
>>> On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:
>>>
>>> External Email - Use Caution
>>> Dear Douglas,
>>>
>>> So, as far as I understand you, if I use a smoothing of 15 I can use a
>>> --cache of 2 in thickness analysis, but I should use a higher --cache for
>>> volume, such as 3. Is that correct?
>>> And would you recommend me using another smoothing level?
>>>
>>> Thank you very much for your help.
>>> Kind regards,
>>>
>>> Agurne
>>>
>>> El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (<
>>> dgr...@mgh.harvard.edu>) escribió:
>>>
>>>> That is ok for thickness, but not for volume
>>>>
>>>> On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
>>>>
>>>> External Email - Use Caution
>>>> Dear Douglas,
>>>>
>>>> I am doing both thickness and GM volume analyses. I am using a
>>>> smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too
>>>> low? And would a --cache of 2 be too low for both thickness and volume
>>>> analyses, or would it be adequate at least for volume analyses?
>>>> Thank you very much.
>>>>
>>>> Best regards,
>>>>
>>>> Agurne
>>>>
>>>>
>>>>
>>>> Neuropsychology of Severe Medical Conditions Research Team
>>>>
>>>> Dpt of Methods and Experimental Psychology
>>>> Faculty of Psychology and Education
>>>>
>>>> University of Deusto
>>>>
>>>> neurolab.deusto.es
>>>> <http://secure-web.cisco.com/13eL9VR1VrodsUjbGEsZKkii7H_4oFZ6JxkEjznjOHcNJSomvo7PoohKYqpfxYid2YLiqoCqS5t8lJJ8k7SGmRZW-Rrm49cqfk_FsYsh7lkHSA9hqJ4ZxCfKQvg098WrxcBQpfdHuiHniE4q0YxaN-oJGKdXw3at7j8wpNKKd1s0brILkj9hn70avIjpNZuR5rOGF4V_HoqoIoUMMn-Usc5TK09H0PoLHqXRJwtTE6xtDfrtLLG4yfDvmLs3bJM5JwAJWOMKclbenIec2VPBKjw/http%3A%2F%2Fneurolab.deusto.es%2F>
>>>>
>>>>
>>>>
>>>> Avda. de las Universidades 24,
>>>>
>>>> 48007, Bilbao (Spain)
>>>>
>>>> Phone: +34 944139000 (ext. 3015)
>>>>
>>>>
>>>> El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (<
>>>> dgr...@mgh.harvard.edu>) escrib

Re: [Freesurfer] multiple comparisons correction

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,

I have another question regarding multiple comparisons correction:

Can I use --cache  with volume analyses? Or should I use --grf?


Thank you very much,

Kind regards,


Agurne


El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (<
a.sampe...@deusto.es>) escribió:

> Dear Douglas,
> Thank you very much ! This paper is very helpful.
> Regards,
>
> Agurne
>
>
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
>
> El mar, 9 feb 2021 a las 17:55, Douglas N. Greve ()
> escribió:
>
>> Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of
>> this paper
>>
>> False positive rates in surface-based anatomical analysis
>> Douglas N. Greve a, b, * , Bruce Fischl a, b
>>
>> On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:
>>
>> External Email - Use Caution
>> Dear Douglas,
>>
>> So, as far as I understand you, if I use a smoothing of 15 I can use a
>> --cache of 2 in thickness analysis, but I should use a higher --cache for
>> volume, such as 3. Is that correct?
>> And would you recommend me using another smoothing level?
>>
>> Thank you very much for your help.
>> Kind regards,
>>
>> Agurne
>>
>> El mar, 9 feb 2021 a las 17:44, Douglas N. Greve ()
>> escribió:
>>
>>> That is ok for thickness, but not for volume
>>>
>>> On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
>>>
>>> External Email - Use Caution
>>> Dear Douglas,
>>>
>>> I am doing both thickness and GM volume analyses. I am using a smoothing
>>> of 15. With a smoothing of 15, would a --cache of 2 be still too low? And
>>> would a --cache of 2 be too low for both thickness and volume analyses,
>>> or would it be adequate at least for volume analyses?
>>> Thank you very much.
>>>
>>> Best regards,
>>>
>>> Agurne
>>>
>>>
>>>
>>> Neuropsychology of Severe Medical Conditions Research Team
>>>
>>> Dpt of Methods and Experimental Psychology
>>> Faculty of Psychology and Education
>>>
>>> University of Deusto
>>>
>>> neurolab.deusto.es
>>> <http://secure-web.cisco.com/13eL9VR1VrodsUjbGEsZKkii7H_4oFZ6JxkEjznjOHcNJSomvo7PoohKYqpfxYid2YLiqoCqS5t8lJJ8k7SGmRZW-Rrm49cqfk_FsYsh7lkHSA9hqJ4ZxCfKQvg098WrxcBQpfdHuiHniE4q0YxaN-oJGKdXw3at7j8wpNKKd1s0brILkj9hn70avIjpNZuR5rOGF4V_HoqoIoUMMn-Usc5TK09H0PoLHqXRJwtTE6xtDfrtLLG4yfDvmLs3bJM5JwAJWOMKclbenIec2VPBKjw/http%3A%2F%2Fneurolab.deusto.es%2F>
>>>
>>>
>>>
>>> Avda. de las Universidades 24,
>>>
>>> 48007, Bilbao (Spain)
>>>
>>> Phone: +34 944139000 (ext. 3015)
>>>
>>>
>>> El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (<
>>> dgr...@mgh.harvard.edu>) escribió:
>>>
>>>>
>>>>
>>>> On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
>>>>
>>>> External Email - Use Caution
>>>> Dear Freesurfer experts,
>>>>
>>>> I am doing a longitudinal repeated measures ANOVA 2x2, with two
>>>> groups (experimental vs control) and two time points (pre and post
>>>> treatment).
>>>>
>>>> I have followed the group analysis tutorial ( *MailScanner has
>>>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
>>>> be*
>>>> https://secure-web.cisco.com/1_wpkFmQ6nZFQp0yOHorX-pT7wGKx8HuLLx3_ANldnkgimrrke655sS8_odVLrHOMF1sCD6w_X9d1TmkTFJLSVh-qDczJ4CjBplvty9AyQWIdm1QhO2FV_6iJntX625PVj8IgkFhM7HOzf054WYoArZnRHjHBZuw-4jF0E2lcLOClsKPMSl9xelIZeWSQMqmonU9kwO8cOoWwVNm96Y6atVuy4AwWgirvYLGBm1dxpcEctshQB4JVVqEKLsHkNOvxgPXXvXPOzt4v-xfWX2F00w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29
>>>> <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.

Re: [Freesurfer] multiple comparisons correction

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,
Thank you very much ! This paper is very helpful.
Regards,

Agurne





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El mar, 9 feb 2021 a las 17:55, Douglas N. Greve ()
escribió:

> Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of
> this paper
>
> False positive rates in surface-based anatomical analysis
> Douglas N. Greve a, b, * , Bruce Fischl a, b
>
> On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> So, as far as I understand you, if I use a smoothing of 15 I can use a
> --cache of 2 in thickness analysis, but I should use a higher --cache for
> volume, such as 3. Is that correct?
> And would you recommend me using another smoothing level?
>
> Thank you very much for your help.
> Kind regards,
>
> Agurne
>
> El mar, 9 feb 2021 a las 17:44, Douglas N. Greve ()
> escribió:
>
>> That is ok for thickness, but not for volume
>>
>> On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
>>
>> External Email - Use Caution
>> Dear Douglas,
>>
>> I am doing both thickness and GM volume analyses. I am using a smoothing
>> of 15. With a smoothing of 15, would a --cache of 2 be still too low? And
>> would a --cache of 2 be too low for both thickness and volume analyses,
>> or would it be adequate at least for volume analyses?
>> Thank you very much.
>>
>> Best regards,
>>
>> Agurne
>>
>>
>>
>> Neuropsychology of Severe Medical Conditions Research Team
>>
>> Dpt of Methods and Experimental Psychology
>> Faculty of Psychology and Education
>>
>> University of Deusto
>>
>> neurolab.deusto.es
>> <http://secure-web.cisco.com/13eL9VR1VrodsUjbGEsZKkii7H_4oFZ6JxkEjznjOHcNJSomvo7PoohKYqpfxYid2YLiqoCqS5t8lJJ8k7SGmRZW-Rrm49cqfk_FsYsh7lkHSA9hqJ4ZxCfKQvg098WrxcBQpfdHuiHniE4q0YxaN-oJGKdXw3at7j8wpNKKd1s0brILkj9hn70avIjpNZuR5rOGF4V_HoqoIoUMMn-Usc5TK09H0PoLHqXRJwtTE6xtDfrtLLG4yfDvmLs3bJM5JwAJWOMKclbenIec2VPBKjw/http%3A%2F%2Fneurolab.deusto.es%2F>
>>
>>
>>
>> Avda. de las Universidades 24,
>>
>> 48007, Bilbao (Spain)
>>
>> Phone: +34 944139000 (ext. 3015)
>>
>>
>> El mar, 9 feb 2021 a las 15:46, Douglas N. Greve ()
>> escribió:
>>
>>>
>>>
>>> On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
>>>
>>> External Email - Use Caution
>>> Dear Freesurfer experts,
>>>
>>> I am doing a longitudinal repeated measures ANOVA 2x2, with two
>>> groups (experimental vs control) and two time points (pre and post
>>> treatment).
>>>
>>> I have followed the group analysis tutorial ( *MailScanner has detected
>>> a possible fraud attempt from "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1YYXPkjCyzOxcthjmbe9eEO8POSyi-gHOxWGS_5KIwRmlx89maJLGutt5Gw7etIe1PfQl1OPACJFV1otDHbKJVSPNGWRc_s3Vjj3CzIwyuCDxsmiHrn_OLFIFMM0iC0biNcWeb747axOXT2-QSE7opW2kWTDVNw7cuF_Xx85VUas1p_H-yWvFqLyXVzlMo419411MbiZ9ldSNoc9-jsuLlMtMHVh5kgpLFRj6cVRcHkZmjkF8qGz6nBEGq7TBNzTmzNzQwQRT01bFWPQxtN2Kug/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29
>>> <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29>
>>> ), where it is suggested to do a Z Monte Carlo simulation with the
>>> following command:
>>> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp
>>> 0.05\ --2spaces
>>> However, I have two questions regarding this issue:
>>> 1) I would like to know whether is it correct to use for example --cache
>>> 3 or 2 instead of 4. Is it recommended?
>>>
>>> Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low;
>>> also depends on the smoothing level.
>>>
>>> 2) Is it better to use, instead of the above Z Monte Carlo simulation
>>> command, a permutation with the following command?: mri_glmfit-sim \ 
>>> --glmdir
>>> lh.ge

Re: [Freesurfer] multiple comparisons correction

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,

So, as far as I understand you, if I use a smoothing of 15 I can use a
--cache of 2 in thickness analysis, but I should use a higher --cache for
volume, such as 3. Is that correct?
And would you recommend me using another smoothing level?

Thank you very much for your help.
Kind regards,

Agurne

El mar, 9 feb 2021 a las 17:44, Douglas N. Greve ()
escribió:

> That is ok for thickness, but not for volume
>
> On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> I am doing both thickness and GM volume analyses. I am using a smoothing
> of 15. With a smoothing of 15, would a --cache of 2 be still too low? And
> would a --cache of 2 be too low for both thickness and volume analyses,
> or would it be adequate at least for volume analyses?
> Thank you very much.
>
> Best regards,
>
> Agurne
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
> <http://secure-web.cisco.com/13eL9VR1VrodsUjbGEsZKkii7H_4oFZ6JxkEjznjOHcNJSomvo7PoohKYqpfxYid2YLiqoCqS5t8lJJ8k7SGmRZW-Rrm49cqfk_FsYsh7lkHSA9hqJ4ZxCfKQvg098WrxcBQpfdHuiHniE4q0YxaN-oJGKdXw3at7j8wpNKKd1s0brILkj9hn70avIjpNZuR5rOGF4V_HoqoIoUMMn-Usc5TK09H0PoLHqXRJwtTE6xtDfrtLLG4yfDvmLs3bJM5JwAJWOMKclbenIec2VPBKjw/http%3A%2F%2Fneurolab.deusto.es%2F>
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
>
> El mar, 9 feb 2021 a las 15:46, Douglas N. Greve ()
> escribió:
>
>>
>>
>> On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer experts,
>>
>> I am doing a longitudinal repeated measures ANOVA 2x2, with two
>> groups (experimental vs control) and two time points (pre and post
>> treatment).
>>
>> I have followed the group analysis tutorial ( *MailScanner has detected
>> a possible fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1gUhAGwIcIwg0D0GDpPhB3YT_PiU6nUgQhmrC09LKHkoyNOyxheS-NGSyevqLnR2ABCv6w8Yg-zXs-HQpbC1FrvOM5DpYo6WcO2feuOWK5XikoRGayygp1MIpcySFXDvY-ufUtWk_HmQZ1WZMsLpkoh_d9fYWZlZEMM2D-puNJsFlp0uTkt1alk4ONkq-NnuKY3i-8b7FMPhHqCOnsBa6A7iP0a2g0DYzdwen7Zt4Xr6tZv21n4pI7TViGhylhrBhTnrX-FZhRXf783prBdxAYw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29
>> <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29>
>> ), where it is suggested to do a Z Monte Carlo simulation with the
>> following command:
>> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp
>> 0.05\ --2spaces
>> However, I have two questions regarding this issue:
>> 1) I would like to know whether is it correct to use for example --cache
>> 3 or 2 instead of 4. Is it recommended?
>>
>> Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low;
>> also depends on the smoothing level.
>>
>> 2) Is it better to use, instead of the above Z Monte Carlo simulation
>> command, a permutation with the following command?: mri_glmfit-sim \ --glmdir
>> lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg
>> 1
>>
>> The permutation will be more accurate, but at a threshold of 4, it
>> probably won't matter much. But the good thing about permutation is that
>> you can drop the threshold to 3 or 2 or even 1.3, and it will still do the
>> right thing.
>>
>>
>> Is it appropriate to use any of both? I do not know which is more
>> recommended or whether both are adequate so I can simply choose, for
>> example, the first one.
>>
>> Thank you very much in advance.
>>
>> Kind regards,
>>
>> Agurne
>>
>>
>>
>> Neuropsychology of Severe Medical Conditions Research Team
>>
>> Dpt of Methods and Experimental Psychology
>> Faculty of Psychology and Education
>>
>> University of Deusto
>>
>> neurolab.deusto.es
>> <http://secure-web.cisco.com/1UnrLWQpMMxdhKEG5HMrtIxWFxHsJTfrtXypEo9Dc-98NFX_4yPEsg2NqEqoQuReypFHAGq0aXxq1CsKiplAUMhJn3xTUmF95qk9IYP-L7373YTN8T8-RJR55wA1Gnu3iuM

Re: [Freesurfer] multiple comparisons correction

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,

I am doing both thickness and GM volume analyses. I am using a smoothing of
15. With a smoothing of 15, would a --cache of 2 be still too low? And
would a --cache of 2 be too low for both thickness and volume analyses, or
would it be adequate at least for volume analyses?
Thank you very much.

Best regards,

Agurne



Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El mar, 9 feb 2021 a las 15:46, Douglas N. Greve ()
escribió:

>
>
> On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I am doing a longitudinal repeated measures ANOVA 2x2, with two
> groups (experimental vs control) and two time points (pre and post
> treatment).
>
> I have followed the group analysis tutorial ( *MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/126m93QA85w-J22Vo42Au1lb9NHKfXfjy9vO-I9N9Tb9C8_9OolMWndz2yGfvWRu8apjzmmIcClMc_qcqWwJ7vmyAXLbn4fNbSch2L_eLdkgY5xcoA2Ax3xXgr-cTnKW4Aa1y9LnXHlzLGm1phpe2dtVTaFmvzvGWJjb12ZjDreniN5UtVs9Vu2cCfZwDgj2ls4jYZB3idLp7RhC8t2ErQZYAS4BsdHHDH3fqHOucF1WCKZK5D7fH4HPymEFV3oiBZWKH6cboqQSQBUCWPs-QZw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29
> <https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29>
> ), where it is suggested to do a Z Monte Carlo simulation with the
> following command:
> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp
> 0.05\ --2spaces
> However, I have two questions regarding this issue:
> 1) I would like to know whether is it correct to use for example --cache 3
> or 2 instead of 4. Is it recommended?
>
> Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low;
> also depends on the smoothing level.
>
> 2) Is it better to use, instead of the above Z Monte Carlo simulation
> command, a permutation with the following command?: mri_glmfit-sim \ --glmdir
> lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg
> 1
>
> The permutation will be more accurate, but at a threshold of 4, it
> probably won't matter much. But the good thing about permutation is that
> you can drop the threshold to 3 or 2 or even 1.3, and it will still do the
> right thing.
>
>
> Is it appropriate to use any of both? I do not know which is more
> recommended or whether both are adequate so I can simply choose, for
> example, the first one.
>
> Thank you very much in advance.
>
> Kind regards,
>
> Agurne
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
> <http://secure-web.cisco.com/1UnrLWQpMMxdhKEG5HMrtIxWFxHsJTfrtXypEo9Dc-98NFX_4yPEsg2NqEqoQuReypFHAGq0aXxq1CsKiplAUMhJn3xTUmF95qk9IYP-L7373YTN8T8-RJR55wA1Gnu3iuM4MUGQwMR6SqTrWHWlhNVRjSS5BnRoz0lysXBO8ghrHRFlB-03jBzASp5QQha90nwuyk6z1jyP2lupIfhaAxZToPr7Ae2fnuSSJSl8bWpvgdWV6goduAv0Kk67utWKpRwjrBlEZcLB8IsAawzINIA/http%3A%2F%2Fneurolab.deusto.es%2F>
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1o5xCJkmepcQlQQeDkp6QMt3NbIsaoL0dbhkmgt22SqWKRSfgZBAxPHeA7O4N99tdHF4rXvEm-VlzRU1uVUUKRsgcluQ1RKR6_aKY1uaEu6S5VhNQlc6KiG0uqIYJ8ZNhSQeVE-xIiKG5A6FTI_UDmNqJR7WLdVljfcRknEVuO2sT4sqPreQnkeFRLCA9-Munx6OL1PXjdaEO_eccFqIIUMWsL7hnMedvn_RRRnsJS0TwTAwMMhu-9lu8rQVD6Y10JDqDHyxJ0fy45nVqcBhqCA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] multiple comparisons correction

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer experts,

I am doing a longitudinal repeated measures ANOVA 2x2, with two
groups (experimental vs control) and two time points (pre and post
treatment).

I have followed the group analysis tutorial (
https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29
), where it is suggested to do a Z Monte Carlo simulation with the
following command:
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp
0.05\ --2spaces

However, I have two questions regarding this issue:

1) I would like to know whether is it correct to use for example --cache 3
or 2 instead of 4. Is it recommended?

2) Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir
lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1

Is it appropriate to use any of both? I do not know which is more
recommended or whether both are adequate so I can simply choose, for
example, the first one.

Thank you very much in advance.

Kind regards,

Agurne



Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] smooth longitudinal analysis {Disarmed}

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer experts,

I am doing a longitudinal repeated measures analysis and I would like to
know which smooth is better to use (with the mri_surf2surf command).

In the repeated measures guide  (
https://secure-web.cisco.com/1VH4PbpfczyEHmEvf-DmwaQIY3QzK6JXAwbehilCfVS00wb0ePGRglRaMqLwBTNWmPTEbH_5iOxVF9p2fPeZdEF-ZcQX3Sxq_n9oFK0y-PgqiQ_xpmDSa5jfGCgCmHJH5R1IxtK3UEqx3_lgRiHE_yyY49B_kiAOmx8osmc7sC1P5polu2Lu7XOkzEJz7KnSNbvzeF9QKcUWBNhYBMQv3J_TJkZ7RocVkzjt6RuPiLEJtrOH7ToOkEAUCCzK6BcJ0wTlatY1akMFB2aNgWEnHwg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova),
 the
example includes an spatial smooth of 5mm FWHM, but in the group analysis
guide (
https://secure-web.cisco.com/1oS1UIb6CdjIYlaVy9MrNL5Jmb_OznCDVVe5aIhhhjuuRFV-QXM2WugfLnnmeB915cxZ3y2DfoEjF3QKUSDTP-NQi6oXweZ-lLHs0FQdj2jjEv2KAjOdzYqcVaHsRMEWemo31ieC2y48EG-ehOW4EHnZ_j35ObPUXa1k5G11BLAqilaYamlHwTGZea2Sc-htTi4KjPqBI_v2UD7S5U1AZ2NZ9A4ZAd3CXSAyf5VUc84kUub0Oc97khN5or57qLRRUbgyZRN9O6WSiWZNMa0mUBw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0),
the example includes a smooth of 10mm.

Which one would be more appropriate? And, does it depend on the kind of
analysis I am doing (e.g., longitudinal analysis VS a simple group
analysis)?

Thank you very much in advance.

Kind regards,

Agurne Sampedro





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

[Agurne Sampedro Calvete]

External Email - Use Caution

I found it here:
https://secure-web.cisco.com/1Pobz-1CRgeaN25ufKu4UcOwbvjX2LjQiAacXtHLnJRq3FQhxMBarP9V62pvmTN-oTfoNLhHO4A5InMyZX-CjChowd6t4LnXQVq71s1pWtfaI0sRBlnMEein6reZM__dj0bhTOz-ln6_F607244YC4DVDD0Nco3HESUEIMLe4SvbfGSa-LaRnXl2QLem4nS4iHic8qO4tkACjlueIIBYKzg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis

I may have misunderstood.

Thank you very much.

Regards,

Agurne





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El vie., 6 nov. 2020 a las 15:57, Douglas N. Greve ()
escribió:

> Oh, that's an error, you do not have to include --cache-in. Where is that
> page?
>
> On 11/5/2020 10:32 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> Thank you very much for your rapid response. I have another question.
>
> I am following the FS Repeated Measures tutorial and therefore, I ran
> this: mris_preproc --target fsaverage --hemi lh --meas thickness --out
> lh.thickness.mgh --fsgd rmanova.fsgd.
> However, in the  FS Group Analysis tutorial, it says that you must include
> "--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with
> recon-all with the -qcache option, which was my case. As I am doing
> longitudinal analyses, do I have to skip this  option and just follow the
> Repeated Measures tutorial or do I have to include the --cache option?
>
> Thank you very much.
> Best regards,
>
> Agurne
>
>
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
> <http://secure-web.cisco.com/1mlmMbtyefCiLJzS978jSNHK52SkNtXw82_-ayeIvMW-4NwP5LeUX1Oi3tq3WOvTWD5xLqYKVmBT74ttrwlbOPZdJ83V5peA3WPEiR6eluPhb9LMt7TRmisi8apO8qRnjIcN6p5bYnFz2i7EdkVhw3QnwVZ2aqI3kc46Dg8AZGt0-qFoBxCse8MAjUCM9DOlQui5WVtOOZL9_L0LvbVkJHQ/http%3A%2F%2Fneurolab.deusto.es%2F>
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
>
> El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve (<
> dgr...@mgh.harvard.edu>) escribió:
>
>> In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer
>> your question, the first example you give is the right way to handle it.
>>
>>
>> On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:
>>
>> External Email - Use Caution
>> Dear Freesurfer experts,
>>
>> I am trying to do a longitudinal repeated measures ANOVA 2x2, with two
>> groups (experimental vs control) and two time points (pre and post
>> treatment).
>>
>> Although I have run a paired t-test, now I would like to do a repeated
>> measures anova 2x2, since I am doing the same analyses with other data in
>> other softwares.
>>
>> I am trying to follow the tutorial *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1wVu5Gz4iksiDQpw3WC4tPugyfo6UlKc1Cl2Uk8w-z5ecyacsquyV0qU-68vnyygnGZ5iW0U3JiCT8cuT-0PYFtCY0uM9QqGWNk0fyzvLK5iwxb3F3qpx1hrVR1EVrTPlulNOK3QZPF_uaTdx_pd9qcWxIKySbSIJ7Mysranzw_KddhPOlGqThxPB6Vhk3zUUVSBc6n0LOLFxdFB58nCLbw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova
>> <https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova>,
>> but I have several doubts when designing the FSGD file as well as the
>> contrasts.
>>
>> How should it be the FSGD file?
>>
>> I have seen in a previous post the following design for the same number
>> fo groups and time points:
>>
>> GroupDescriptorFile 1
>>
>> Class Subject1
>>
>> Class Subject2
>>
>> Variables Tp1vsTp2.GrExp
>>Tp1vsTp2.GrControl
>>
>> Input   Subject1_time1  Subject1
>> 1 0
>>
>> Input   Subject1_time2  Subject1-1
>> 0
>>
>> Input   Subject2_time1  Subject2
>> 0 1
>>
>> Input   Subject2_time2  Subject02   0
>> -1
>>
>>
>>
>> Design matrix:
>>
>>

Re: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Douglas,

Thank you very much for your rapid response. I have another question.

I am following the FS Repeated Measures tutorial and therefore, I ran
this: mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.thickness.mgh --fsgd rmanova.fsgd.
However, in the  FS Group Analysis tutorial, it says that you must include
"--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with
recon-all with the -qcache option, which was my case. As I am doing
longitudinal analyses, do I have to skip this  option and just follow the
Repeated Measures tutorial or do I have to include the --cache option?

Thank you very much.
Best regards,

Agurne





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve ()
escribió:

> In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer
> your question, the first example you give is the right way to handle it.
>
>
> On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I am trying to do a longitudinal repeated measures ANOVA 2x2, with two
> groups (experimental vs control) and two time points (pre and post
> treatment).
>
> Although I have run a paired t-test, now I would like to do a repeated
> measures anova 2x2, since I am doing the same analyses with other data in
> other softwares.
>
> I am trying to follow the tutorial *MailScanner has detected a possible
> fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/11u6-IyY2-P7w7M4zmGiLCyaG6g2vViEpx4ag8H474t_vAcKQofRlrgzoecVmHS-zCmukHiQ4nYncdNoWgv3qseGeeJ5V9DyPr8qfYwFtrgu7s9OZWm-ZxMwuQ5ZFRq0n-rmVcPAZ0Hk-kzFtomVz5K6pII7oYat7YlIYPSB5e0Ig4auXkKYY9vdGnvAE3T5jbnApRosUxoICfXaCSW4-Fw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova
> <https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova>,
> but I have several doubts when designing the FSGD file as well as the
> contrasts.
>
> How should it be the FSGD file?
>
> I have seen in a previous post the following design for the same number fo
> groups and time points:
>
> GroupDescriptorFile 1
>
> Class Subject1
>
> Class Subject2
>
> Variables Tp1vsTp2.GrExp
>Tp1vsTp2.GrControl
>
> Input   Subject1_time1  Subject1 1
> 0
>
> Input   Subject1_time2  Subject1-10
>
> Input   Subject2_time1  Subject2 0
> 1
>
> Input   Subject2_time2  Subject02   0
> -1
>
>
>
> Design matrix:
>
> 1 0 1 0
>
> 1 0 -1 0
>
> 0 1 0 1
>
> 0 1 0 -1
>
> Contrasts (.mtx files):
> Tp1vsTp2.GrExp0 0 1 0
> Tp1vsTp2.GrControl  0 0 0 -1
> Interaction  0 0 1 -1
>
> Would this design be the correct one to use in this case?
>
> Alternatively, could it be this the correct one?
>
> GroupDescriptorFile 1
>
> Class Subject1
>
> Class Subject2
>
> Variables Tp1vsTp2
>  Groupxtime
>
> Input   Subject1_time1  Subject1 11
>
> Input   Subject1_time2  Subject1-1
> *-1*
>
> Input   Subject2_time1  Subject2 1
> *-1*
>
> Input   Subject2_time2  Subject02   -1  1
>
> Design matrix:
>
> 1 0  1 1
>
> 1 0 -1 -1
>
> 0 1  1 -1
>
> 0 1  -1 1
>
>
>
> Contrasts (.mtx files):
>
> Tp1vsTp20 0 1 0
>
> Groupxtime Interaction   0 0 0 1
>
> Thank you very much in advance.
>
> Kind regards,
>
> Agurne
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
> <http://secure-web.cisco.com/1J2XHqATjb-s81WNLHHOzFHoMov247ukeyY9r_63MCuIYY3b3cgBooSYVXAHcxmruuUhAJRQeOK_M6GhmpQ2HLsoPViHsaOnuQmnS_hX44VhcAXEpVQmkpDhtamFGdp_Y3WSVnP0Hb0VMfltJoov6c0TVAyZfGD7j4wcdLUcORgyyH2uu_WSTkVwMZ87NUx0paSiYbguuSG9LFBN_NCd9ZQ/http%3A%2F%2Fneurolab.deusto.es%2F>
>
>
>
> Avda. de las Universidades 24,
&

Re: [Freesurfer] .mgh file unknown, GLM paired analysis {Disarmed}

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear FS experts,

I have removed the backslashes "\" and now it works, so problem solved.

Thank you very much.

Regards,

Agurne





Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)


El lun., 2 nov. 2020 a las 18:27, Agurne Sampedro Calvete (<
a.sampe...@deusto.es>) escribió:

> Dear Freesurfer Experts,
>
> I am trying to perform a paired analysis in FreeSurfer following this
> tutorial 
> https://secure-web.cisco.com/1GGOE7lAk9DEhVom372ksbhQpoUEm3yIVLX4YqDE8HfMpeOEgVTUnDNdXv_pENZI_Zj8E1pQJo1vbndz8QuwfXZeLFZrg8uFaXPMF0SqFXPUHmLNodW7Jl-SXS-ePsn2uN1wrgmWAb4tMFpdB1JokGuLZFVIqK_lmBvM7eufXwSmiMuSvGQ2NREwZt2mxapAyIqfuj9JwrJS-MUE9Nm4DNw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
>  and I
> have some problems when running the spatially smooth.
>
> I ran the following command:  mri_surf2surf --s fsaverage --hemi lh --fwhm
> 5\ --sval lh.paired-diff.thickness.mgh \ --tval
> lh.paired-diff.thickness.sm05.mgh
>
> And I found this error:
> ERROR: lh.paired-diff.thickness.mgh unknown freesurfer
>
> This file is in my subject directory, but when I see the file properties,
> in the "file type" box it says: unknown. I have read that other users have
> experienced the same error.
>
> What can I do to solve this problem?
>
> Thanks in advance.
>
> Kind regards,
>
> Agurne Sampedro
>
>
>
> Neuropsychology of Severe Medical Conditions Research Team
>
> Dpt of Methods and Experimental Psychology
> Faculty of Psychology and Education
>
> University of Deusto
>
> neurolab.deusto.es
>
>
>
> Avda. de las Universidades 24,
>
> 48007, Bilbao (Spain)
>
> Phone: +34 944139000 (ext. 3015)
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed}

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer experts,

I am trying to do a longitudinal repeated measures ANOVA 2x2, with two
groups (experimental vs control) and two time points (pre and post
treatment).

Although I have run a paired t-test, now I would like to do a repeated
measures anova 2x2, since I am doing the same analyses with other data in
other softwares.

I am trying to follow the tutorial
https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova,
 but I have
several doubts when designing the FSGD file as well as the contrasts.

How should it be the FSGD file?

I have seen in a previous post the following design for the same number fo
groups and time points:

GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables Tp1vsTp2.GrExp
   Tp1vsTp2.GrControl

Input   Subject1_time1  Subject1 1 0

Input   Subject1_time2  Subject1-10

Input   Subject2_time1  Subject2 0
1

Input   Subject2_time2  Subject02   0 -1



Design matrix:

1 0 1 0

1 0 -1 0

0 1 0 1

0 1 0 -1

Contrasts (.mtx files):
Tp1vsTp2.GrExp0 0 1 0
Tp1vsTp2.GrControl  0 0 0 -1
Interaction  0 0 1 -1

Would this design be the correct one to use in this case?

Alternatively, could it be this the correct one?

GroupDescriptorFile 1

Class Subject1

Class Subject2

Variables Tp1vsTp2
 Groupxtime

Input   Subject1_time1  Subject1 11

Input   Subject1_time2  Subject1-1
*-1*

Input   Subject2_time1  Subject2 1
*-1*

Input   Subject2_time2  Subject02   -1  1

Design matrix:

1 0  1 1

1 0 -1 -1

0 1  1 -1

0 1  -1 1



Contrasts (.mtx files):

Tp1vsTp20 0 1 0

Groupxtime Interaction   0 0 0 1

Thank you very much in advance.

Kind regards,

Agurne



Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education

University of Deusto

neurolab.deusto.es



Avda. de las Universidades 24,

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec problems not receiving keyboard input

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer Experts,

Although I haven't had any problems with the qdec until now, this week the
qdec is having some errors when receiving inputs from the keyboard. For
example, I can't write in the design name box, nor can I change the minimum
or maximum threshold in the display page. I've seen that other people have
had a similar problem too. How can I solve it?

Thanks in advance.

Kind regards,
Agurne Sampedro
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer